The code for 2024_09_UCSF_Bulk_EB_Timecourse dataset is in a separate file.

This code file can be applied to all other datasets from 2023_12 release to 2024_09 release.

In each setting, based on the processed output file, take all genes with non-NA adjusted pvalues as genes to consider, and significant genes based on adjusted p-value cutoff 0.05 and absolute log2foldchange cutoff log2(1.5).

R libraries.

library(ggplot2)
library(ggrepel)
library(ggpubr)
library(stringr)
library(RColorBrewer)
library(goseq)
library(fgsea)

library(dplyr)
library(data.table)
theme_set(theme_classic())

# BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene", force=TRUE)
# BiocManager::install("org.Hs.eg.db")
release_name = params$release_name
release_name
## [1] "2023_12_JAX_RNAseq_ExtraEmbryonic"

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "gene_annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "gene_annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

sapply(pathways, length)
## reactome    go_bp 
##     1326     5320

Read in gene annotation

gene_info = fread("data/gencode_v44_primary_assembly_info.tsv", 
                  data.table = FALSE)
dim(gene_info)
## [1] 62754     8
gene_info[1:2,]
##               geneId  chr strand     start       end ensembl_gene_id
## 1 ENSG00000000003.16 chrX      - 100627108 100639991 ENSG00000000003
## 2  ENSG00000000005.6 chrX      + 100584936 100599885 ENSG00000000005
##   hgnc_symbol                                       description
## 1      TSPAN6 tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]
## 2        TNMD   tenomodulin [Source:HGNC Symbol;Acc:HGNC:17757]

Prepare for reading in DE results

result_dir = file.path("results", release_name)
processed_output_dir = file.path(result_dir, "processed")

all_result_files = list.files(path=processed_output_dir, pattern=".tsv", 
                              all.files=TRUE, full.names=FALSE)
all_result_files = sort(all_result_files)

# condition_DE_files is for datasets with hypoxia and normoxia condition comparison
regular_DE_files = all_result_files[!grepl("hyp_vs_nor", all_result_files)]
condition_DE_files = all_result_files[grepl("hyp_vs_nor", all_result_files)]


# extract core strings from regular DE result files

extract_cores <- function(x, str_before, str_after){

  pattern <- paste0(".*", str_before, "(.*?)", str_after, ".*")
  middle_string <- sub(pattern, "\\1", x)
  middle_substrings <- strsplit(middle_string, "_")[[1]]
  x_d_group <- paste(middle_substrings[1:(length(middle_substrings)-1)], 
                     collapse = "_")
  x_gene <- middle_substrings[length(middle_substrings)]
  
  return(c(x_d_group, x_gene))
}

df_file_info = NULL

for (x in regular_DE_files){
  df_file_info = rbind(df_file_info, 
                       extract_cores(x, 
                                    paste0(release_name, "_"), 
                                    "_DEseq2.tsv"))
}

df_file_info = as.data.frame(df_file_info)
colnames(df_file_info) = c("DE_general_group", "gene")

df_file_info$items = paste(df_file_info$DE_general_group, 
                           df_file_info$gene, sep="_")
df_file_info$items
## [1] "ExM_day_6_nor_ISL1"   "PrS_day_6_hyp_EPAS1"  "PrS_day_6_nor_EPAS1" 
## [4] "PrS_day_6_nor_FOSB"   "PrS_day_6_nor_GCM1"   "PrS_day_6_nor_GRHL1" 
## [7] "PrS_day_6_nor_POU2F3" "PrS_day_6_nor_PPARG"
df_file_info
##   DE_general_group   gene                items
## 1    ExM_day_6_nor   ISL1   ExM_day_6_nor_ISL1
## 2    PrS_day_6_hyp  EPAS1  PrS_day_6_hyp_EPAS1
## 3    PrS_day_6_nor  EPAS1  PrS_day_6_nor_EPAS1
## 4    PrS_day_6_nor   FOSB   PrS_day_6_nor_FOSB
## 5    PrS_day_6_nor   GCM1   PrS_day_6_nor_GCM1
## 6    PrS_day_6_nor  GRHL1  PrS_day_6_nor_GRHL1
## 7    PrS_day_6_nor POU2F3 PrS_day_6_nor_POU2F3
## 8    PrS_day_6_nor  PPARG  PrS_day_6_nor_PPARG
# extract core strings from DE result files about hypoxia and normoxia conditions

extract_cores_cond <- function(x, str_before, str_after){

  pattern <- paste0(".*", str_before, "(.*?)", str_after, ".*")
  middle_string <- sub(pattern, "\\1", x)
  middle_substrings <- strsplit(middle_string, "_")[[1]]
  x_d_group <- paste(middle_substrings[1:(length(middle_substrings)-3)], 
                     collapse = "_")
  x_compare <- paste(middle_substrings[(length(middle_substrings)-2):length(middle_substrings)], 
                     collapse = "_")
  
  return(c(x_d_group, x_compare))
}

if (length(condition_DE_files)>0){
  
  df_file_info_cond = NULL
  
  for (x in condition_DE_files){
    df_file_info_cond = rbind(df_file_info_cond, 
                              extract_cores_cond(x, 
                                                 paste0(release_name, "_"), 
                                                 "_DEseq2.tsv"))
  }
  
  df_file_info_cond = as.data.frame(df_file_info_cond)
  colnames(df_file_info_cond) = c("DE_general_group", "comparison")
  
  df_file_info_cond$items = paste(df_file_info_cond$DE_general_group, 
                             df_file_info_cond$comparison, sep="_")
  print(df_file_info_cond$items)
  print(df_file_info_cond)
}
## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor"  "PrS_day_6_EPAS1_KO_hyp_vs_nor" 
## [3] "PrS_day_6_EPAS1_PTC_hyp_vs_nor" "PrS_day_6_WT_WT_hyp_vs_nor"    
##      DE_general_group comparison                          items
## 1  PrS_day_6_EPAS1_CE hyp_vs_nor  PrS_day_6_EPAS1_CE_hyp_vs_nor
## 2  PrS_day_6_EPAS1_KO hyp_vs_nor  PrS_day_6_EPAS1_KO_hyp_vs_nor
## 3 PrS_day_6_EPAS1_PTC hyp_vs_nor PrS_day_6_EPAS1_PTC_hyp_vs_nor
## 4     PrS_day_6_WT_WT hyp_vs_nor     PrS_day_6_WT_WT_hyp_vs_nor
# set an exception for UCSF data

Read in DE results and conduct enrichment analysis

Regular DE results

fc0 = log2(1.5)
p0  = 0.05

max_n2kp = 10
goseq_res = NULL

ko_start_col_index = 7

for (i in 1:nrow(df_file_info)){
  
  it1 = df_file_info$items[i]
  gene_name = df_file_info$gene[i]
    
  res = fread(paste0("results/", release_name, "/processed/", release_name, 
                     "_", it1, "_DEseq2.tsv"), 
              data.table = FALSE)
  res[1:2,]
  
  de_info_columns = colnames(res)[ko_start_col_index:ncol(res)]
  strategy_vec = sapply(de_info_columns, function(x)strsplit(x, "_")[[1]][2])
  unique_strategies = unique(strategy_vec)
  
  for (ko1 in unique_strategies){
    
    print(paste0(it1, " ", ko1))
    
    de_gene_sets = list()
      
    res_k = res[,c(1, grep(ko1, names(res)))]
    names(res_k) = gsub(paste0(gene_name, "_", ko1, "_"), "", names(res_k))
    
    res_k = res_k[!is.na(res_k$padj),]

    ww_up = which((res_k$log2FoldChange > fc0) & (res_k$padj < p0))
    ww_down = which((res_k$log2FoldChange < ((-1)*fc0)) & (res_k$padj < p0))

    de_gene_sets[[paste0(ko1, "_up")]] = res_k[ww_up,]$gene_ID
    de_gene_sets[[paste0(ko1, "_down")]] = res_k[ww_down,]$gene_ID

    print(sapply(de_gene_sets, length))
    
    print(table(res_k$gene_ID %in% gene_info$ensembl_gene_id))
  
    gene_info_k = gene_info[gene_info$ensembl_gene_id %in% res_k$gene_ID,]
    dim(gene_info_k)
    gene_info_k[1:2,]
    
    sum(is.na(gene_info_k$hgnc_symbol))
    
    t_symbol = table(gene_info_k$hgnc_symbol)
    table(t_symbol)
    t_symbol[t_symbol > 1]
    
    gene_info_k = gene_info_k[gene_info_k$hgnc_symbol %in% names(t_symbol)[t_symbol==1],]
    dim(gene_info_k)
     
    for(j in 1:length(de_gene_sets)){
      if(length(de_gene_sets[[j]]) < 10) { next }
    
      print(j)
      set_j = names(de_gene_sets)[j]
  
      genes = gene_info_k$ensembl_gene_id %in% de_gene_sets[[j]]
      names(genes) = gene_info_k$hgnc_symbol
      table(genes)
    
      pwf = nullp(genes, "hg38", "geneSymbol")
  
      for(k1 in names(pathways)){
        p1 = pathways[[k1]]
        res1 = goseq(pwf, "hg38", "geneSymbol", 
                     gene2cat=goseq:::reversemapping(p1))
        res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
      
        nD = sum(res1$FDR < 0.05)
      
        if(nD > 0){
          res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
          res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
          res1$category = gsub("_", " ", res1$category)
          res1$category = tolower(res1$category)
          res1$category = substr(res1$category, start=1, stop=120)
          set_j_fullname = paste0(it1, "_", set_j)
          goseq_res[[set_j_fullname]][[k1]] = res1
        }
      }
    }
    
  }

}
## [1] "ExM_day_6_nor_ISL1 CE"
##   CE_up CE_down 
##     340     312 
## 
##  TRUE 
## 16874 
## [1] 1

## [1] 2

## [1] "ExM_day_6_nor_ISL1 KO"
##   KO_up KO_down 
##     165     240 
## 
##  TRUE 
## 15502 
## [1] 1

## [1] 2

## [1] "ExM_day_6_nor_ISL1 PTC"
##   PTC_up PTC_down 
##      181      251 
## 
##  TRUE 
## 16422 
## [1] 1

## [1] 2

## [1] "PrS_day_6_hyp_EPAS1 CE"
##   CE_up CE_down 
##    2266    1930 
## 
##  TRUE 
## 18336 
## [1] 1

## [1] 2

## [1] "PrS_day_6_hyp_EPAS1 KO"
##   KO_up KO_down 
##    1306     834 
## 
##  TRUE 
## 17892 
## [1] 1

## [1] 2

## [1] "PrS_day_6_hyp_EPAS1 PTC"
##   PTC_up PTC_down 
##     1547     1006 
## 
##  TRUE 
## 17893 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_EPAS1 CE"
##   CE_up CE_down 
##     769     603 
## 
##  TRUE 
## 16172 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_EPAS1 KO"
##   KO_up KO_down 
##      18      22 
## 
##  TRUE 
## 11649 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_EPAS1 PTC"
##   PTC_up PTC_down 
##      143      161 
## 
##  TRUE 
## 14825 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_FOSB CE"
##   CE_up CE_down 
##     361      48 
## 
##  TRUE 
## 16627 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_FOSB KO"
##   KO_up KO_down 
##     591     256 
## 
##  TRUE 
## 17502 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_FOSB PTC"
##   PTC_up PTC_down 
##       87       34 
## 
##  TRUE 
## 16628 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GCM1 CE"
##   CE_up CE_down 
##    2263    3036 
## 
##  TRUE 
## 18923 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GCM1 KO"
##   KO_up KO_down 
##    1782    2704 
## 
##  TRUE 
## 18929 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GCM1 PTC"
##   PTC_up PTC_down 
##     1656     2599 
## 
##  TRUE 
## 18979 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GRHL1 CE"
##   CE_up CE_down 
##    1384    2055 
## 
##  TRUE 
## 18937 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GRHL1 KO"
##   KO_up KO_down 
##    1034    1449 
## 
##  TRUE 
## 18874 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_GRHL1 PTC"
##   PTC_up PTC_down 
##     2355     2740 
## 
##  TRUE 
## 18989 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_POU2F3 CE"
##   CE_up CE_down 
##     940    1098 
## 
##  TRUE 
## 17488 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_POU2F3 KO"
##   KO_up KO_down 
##     365     225 
## 
##  TRUE 
## 14825 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_POU2F3 PTC"
##   PTC_up PTC_down 
##        2        4 
## 
##  TRUE 
## 18988 
## [1] "PrS_day_6_nor_PPARG CE"
##   CE_up CE_down 
##    2207    2296 
## 
##  TRUE 
## 19064 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_PPARG KO"
##   KO_up KO_down 
##    1395    1634 
## 
##  TRUE 
## 18880 
## [1] 1

## [1] 2

## [1] "PrS_day_6_nor_PPARG PTC"
##   PTC_up PTC_down 
##     1672     2342 
## 
##  TRUE 
## 19033 
## [1] 1

## [1] 2

### DE results about hypoxia vs normoxia conditions if available

## Keep using the same 
## goseq_res
## object

if (length(condition_DE_files)>0){
    
  fc0 = log2(1.5)
  p0  = 0.05
  
  max_n2kp = 10
  
  ko_start_col_index = 7
  
  for (i in 1:nrow(df_file_info_cond)){
    
    it1 = df_file_info_cond$items[i]
    compare_name = df_file_info_cond$comparison[i]
    print(compare_name)
    
    res = fread(paste0("results/", release_name, "/processed/", release_name, 
                       "_", it1, "_DEseq2.tsv"), 
                data.table = FALSE)
    res[1:2,]
    
    de_info_columns = colnames(res)[ko_start_col_index:ncol(res)]
    
    de_gene_sets = list()
        
    res_k = res[,c(1, grep(compare_name, names(res)))]
    names(res_k) = gsub(paste0(compare_name, "_"), "", names(res_k))
      
    res_k = res_k[!is.na(res_k$padj),]
  
    ww_up = which((res_k$log2FoldChange > fc0) & (res_k$padj < p0))
    ww_down = which((res_k$log2FoldChange < ((-1)*fc0)) & (res_k$padj < p0))
  
    de_gene_sets[[paste0("up")]] = res_k[ww_up,]$gene_ID
    de_gene_sets[[paste0("down")]] = res_k[ww_down,]$gene_ID
  
    print(sapply(de_gene_sets, length))
    
    print(table(res_k$gene_ID %in% gene_info$ensembl_gene_id))
  
    gene_info_k = gene_info[gene_info$ensembl_gene_id %in% res_k$gene_ID,]
    dim(gene_info_k)
    gene_info_k[1:2,]
    
    sum(is.na(gene_info_k$hgnc_symbol))
    
    t_symbol = table(gene_info_k$hgnc_symbol)
    table(t_symbol)
    t_symbol[t_symbol > 1]
    
    gene_info_k = gene_info_k[gene_info_k$hgnc_symbol %in% names(t_symbol)[t_symbol==1],]
    dim(gene_info_k)
       
    for(j in 1:length(de_gene_sets)){
      if(length(de_gene_sets[[j]]) < 10) { next }
    
      print(j)
      set_j = names(de_gene_sets)[j]
  
      genes = gene_info_k$ensembl_gene_id %in% de_gene_sets[[j]]
      names(genes) = gene_info_k$hgnc_symbol
      table(genes)
    
      pwf = nullp(genes, "hg38", "geneSymbol")
  
      for(k1 in names(pathways)){
        p1 = pathways[[k1]]
        res1 = goseq(pwf, "hg38", "geneSymbol", 
                     gene2cat=goseq:::reversemapping(p1))
        res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
      
        nD = sum(res1$FDR < 0.05)
      
        if(nD > 0){
          res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
          res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
          res1$category = gsub("_", " ", res1$category)
          res1$category = tolower(res1$category)
          res1$category = substr(res1$category, start=1, stop=120)
          set_j_fullname = paste0(it1, "_", set_j)
          goseq_res[[set_j_fullname]][[k1]] = res1
        }
      }
    }
      
  }

}
## [1] "hyp_vs_nor"
##   up down 
## 1894 1624 
## 
##  TRUE 
## 15660 
## [1] 1

## [1] 2

## [1] "hyp_vs_nor"
##   up down 
## 1216 1302 
## 
##  TRUE 
## 15018 
## [1] 1

## [1] 2

## [1] "hyp_vs_nor"
##   up down 
## 1855 1809 
## 
##  TRUE 
## 16546 
## [1] 1

## [1] 2

## [1] "hyp_vs_nor"
##   up down 
## 3324 3400 
## 
##  TRUE 
## 19162 
## [1] 1

## [1] 2

Save results out

names(goseq_res)
##  [1] "ExM_day_6_nor_ISL1_CE_up"            "ExM_day_6_nor_ISL1_CE_down"         
##  [3] "ExM_day_6_nor_ISL1_KO_up"            "ExM_day_6_nor_ISL1_KO_down"         
##  [5] "ExM_day_6_nor_ISL1_PTC_up"           "ExM_day_6_nor_ISL1_PTC_down"        
##  [7] "PrS_day_6_hyp_EPAS1_CE_up"           "PrS_day_6_hyp_EPAS1_CE_down"        
##  [9] "PrS_day_6_hyp_EPAS1_KO_up"           "PrS_day_6_hyp_EPAS1_KO_down"        
## [11] "PrS_day_6_hyp_EPAS1_PTC_up"          "PrS_day_6_hyp_EPAS1_PTC_down"       
## [13] "PrS_day_6_nor_EPAS1_CE_up"           "PrS_day_6_nor_EPAS1_CE_down"        
## [15] "PrS_day_6_nor_EPAS1_PTC_up"          "PrS_day_6_nor_FOSB_CE_up"           
## [17] "PrS_day_6_nor_FOSB_KO_up"            "PrS_day_6_nor_FOSB_PTC_up"          
## [19] "PrS_day_6_nor_GCM1_CE_up"            "PrS_day_6_nor_GCM1_CE_down"         
## [21] "PrS_day_6_nor_GCM1_KO_up"            "PrS_day_6_nor_GCM1_KO_down"         
## [23] "PrS_day_6_nor_GCM1_PTC_up"           "PrS_day_6_nor_GCM1_PTC_down"        
## [25] "PrS_day_6_nor_GRHL1_CE_up"           "PrS_day_6_nor_GRHL1_CE_down"        
## [27] "PrS_day_6_nor_GRHL1_KO_up"           "PrS_day_6_nor_GRHL1_KO_down"        
## [29] "PrS_day_6_nor_GRHL1_PTC_up"          "PrS_day_6_nor_GRHL1_PTC_down"       
## [31] "PrS_day_6_nor_POU2F3_CE_up"          "PrS_day_6_nor_POU2F3_CE_down"       
## [33] "PrS_day_6_nor_POU2F3_KO_up"          "PrS_day_6_nor_PPARG_CE_up"          
## [35] "PrS_day_6_nor_PPARG_CE_down"         "PrS_day_6_nor_PPARG_KO_up"          
## [37] "PrS_day_6_nor_PPARG_KO_down"         "PrS_day_6_nor_PPARG_PTC_up"         
## [39] "PrS_day_6_nor_PPARG_PTC_down"        "PrS_day_6_EPAS1_CE_hyp_vs_nor_up"   
## [41] "PrS_day_6_EPAS1_CE_hyp_vs_nor_down"  "PrS_day_6_EPAS1_KO_hyp_vs_nor_up"   
## [43] "PrS_day_6_EPAS1_KO_hyp_vs_nor_down"  "PrS_day_6_EPAS1_PTC_hyp_vs_nor_up"  
## [45] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_down" "PrS_day_6_WT_WT_hyp_vs_nor_up"      
## [47] "PrS_day_6_WT_WT_hyp_vs_nor_down"
for(n1 in names(goseq_res)){
  print(n1)
  print(goseq_res[[n1]])
}
## [1] "ExM_day_6_nor_ISL1_CE_up"
## $reactome
##                                category over_represented_pvalue
## 525          interferon gamma signaling            2.796105e-06
## 384 formation of the cornified envelope            4.223776e-06
## 572                      keratinization            5.143913e-06
## 524     interferon alpha beta signaling            1.151508e-04
##     under_represented_pvalue numDEInCat numInCat         FDR
## 525                0.9999996         11       73 0.002271895
## 384                0.9999996          8       37 0.002271895
## 572                0.9999996          8       38 0.002271895
## 524                0.9999838          8       58 0.038143700
## 
## $go_bp
##                                                category over_represented_pvalue
## 1502                                leukocyte migration            3.124554e-06
## 2914            positive regulation of defense response            7.945702e-06
## 4728                     response to type ii interferon            9.460662e-06
## 717                        defense response to symbiont            1.112058e-05
## 555             cellular response to type ii interferon            1.142714e-05
## 39                          acute inflammatory response            1.264366e-05
## 4523              regulation of vasculature development            1.769723e-05
## 2789 positive regulation of acute inflammatory response            2.019111e-05
## 1893                        myeloid leukocyte migration            2.306438e-05
## 1824                         mononuclear cell migration            2.489424e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 1502                0.9999992         19      242 0.01120439
## 2914                0.9999977         22      336 0.01120439
## 4728                0.9999985         11       94 0.01120439
## 717                 0.9999971         18      241 0.01120439
## 555                 0.9999984         10       78 0.01120439
## 39                  0.9999985          9       63 0.01120439
## 4523                0.9999955         17      225 0.01323627
## 2789                0.9999992          5       16 0.01323627
## 1893                0.9999953         13      143 0.01323627
## 1824                0.9999953         12      122 0.01323627
## 
## [1] "ExM_day_6_nor_ISL1_CE_down"
## $reactome
##                                                         category
## 345                            extracellular matrix organization
## 306                                            ecm proteoglycans
## 608                                 met activates ptk2 signaling
## 252                      degradation of the extracellular matrix
## 428                         germ layer formation at gastrulation
## 183                                 collagen chain trimerization
## 611                                   met promotes cell motility
## 84  assembly of collagen fibrils and other multimeric structures
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345            4.300776e-09                1.0000000         23      234
## 306            5.939069e-06                0.9999994          9       59
## 608            3.428814e-05                0.9999976          6       28
## 252            5.036838e-05                0.9999907         11      108
## 428            8.027500e-05                0.9999973          4       12
## 183            1.777108e-04                0.9999823          6       37
## 611            2.203652e-04                0.9999770          6       39
## 84             2.284038e-04                0.9999699          7       51
##              FDR
## 345 5.698528e-06
## 306 3.934633e-03
## 608 1.514393e-02
## 252 1.668453e-02
## 428 2.127288e-02
## 183 3.782939e-02
## 611 3.782939e-02
## 84  3.782939e-02
## 
## $go_bp
##                                           category over_represented_pvalue
## 876          embryonic skeletal system development            1.798390e-11
## 4552                      renal system development            6.187987e-10
## 367                     cardiocyte differentiation            4.307276e-09
## 371                          cartilage development            4.908175e-09
## 5000            striated muscle tissue development            1.128264e-08
## 948                  epithelial cell proliferation            1.725666e-08
## 165                        appendage morphogenesis            2.166131e-08
## 877        embryonic skeletal system morphogenesis            2.818212e-08
## 3896   regulation of epithelial cell proliferation            3.020359e-08
## 1022 external encapsulating structure organization            5.393876e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 876                         1         17       91 9.562041e-08
## 4552                        1         27      274 1.645076e-06
## 367                         1         17      122 6.524191e-06
## 371                         1         19      162 6.524191e-06
## 5000                        1         21      201 1.199796e-05
## 948                         1         28      352 1.529228e-05
## 165                         1         16      122 1.645332e-05
## 877                         1         12       66 1.784361e-05
## 3896                        1         25      295 1.784361e-05
## 1022                        1         23      261 2.867924e-05
## 
## [1] "ExM_day_6_nor_ISL1_KO_up"
## $reactome
##                            category over_represented_pvalue
## 524 interferon alpha beta signaling            8.529484e-06
## 525      interferon gamma signaling            4.379451e-05
## 773    peptide hormone biosynthesis            5.067351e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 524                0.9999993          7       54 0.01130157
## 525                0.9999956          7       69 0.02238080
## 773                0.9999995          3        6 0.02238080
## 
## $go_bp
##                                                category over_represented_pvalue
## 2914            positive regulation of defense response            2.469644e-09
## 39                          acute inflammatory response            2.504879e-07
## 4008               regulation of innate immune response            3.072348e-07
## 41                                 acute phase response            3.369740e-07
## 4679           response to molecule of bacterial origin            3.958030e-07
## 717                        defense response to symbiont            4.643181e-07
## 4362        regulation of response to cytokine stimulus            4.798123e-07
## 3257 positive regulation of response to biotic stimulus            1.206691e-06
## 555             cellular response to type ii interferon            2.734116e-06
## 4734                                  response to virus            2.849596e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 2914                1.0000000         19      306 0.0000131311
## 39                  1.0000000          8       56 0.0003644517
## 4008                0.9999999         16      294 0.0003644517
## 41                  1.0000000          6       25 0.0003644517
## 4679                0.9999999         14      227 0.0003644517
## 717                 0.9999999         14      230 0.0003644517
## 4362                0.9999999         11      135 0.0003644517
## 3257                0.9999998         14      249 0.0008019969
## 555                 0.9999998          8       76 0.0015151303
## 4734                0.9999994         15      307 0.0015151303
## 
## [1] "ExM_day_6_nor_ISL1_KO_down"
## $reactome
##                                    category over_represented_pvalue
## 345       extracellular matrix organization            3.032496e-09
## 306                       ecm proteoglycans            4.830913e-06
## 252 degradation of the extracellular matrix            1.872737e-05
## 673                      ncam1 interactions            9.464331e-05
##     under_represented_pvalue numDEInCat numInCat          FDR
## 345                1.0000000         20      226 4.018057e-06
## 306                0.9999996          8       56 3.200480e-03
## 252                0.9999972         10      103 8.271254e-03
## 673                0.9999940          5       28 3.135060e-02
## 
## $go_bp
##                                     category over_represented_pvalue
## 876    embryonic skeletal system development            7.574622e-13
## 4850              sensory system development            6.910581e-11
## 869              embryonic organ development            8.799471e-11
## 877  embryonic skeletal system morphogenesis            3.542110e-10
## 5000      striated muscle tissue development            7.906715e-10
## 367               cardiocyte differentiation            8.514814e-10
## 1877               muscle tissue development            9.403096e-10
## 371                    cartilage development            3.662875e-09
## 165                  appendage morphogenesis            4.066712e-09
## 335                 cardiac cell development            5.731365e-09
##      under_represented_pvalue numDEInCat numInCat          FDR
## 876                         1         16       80 4.027426e-09
## 4850                        1         26      287 1.559560e-07
## 869                         1         27      329 1.559560e-07
## 877                         1         12       57 4.708350e-07
## 5000                        1         20      195 7.142323e-07
## 367                         1         16      119 7.142323e-07
## 1877                        1         25      316 7.142323e-07
## 371                         1         17      156 2.402523e-06
## 165                         1         15      118 2.402523e-06
## 335                         1         12       68 3.047367e-06
## 
## [1] "ExM_day_6_nor_ISL1_PTC_up"
## $reactome
##                         category over_represented_pvalue
## 773 peptide hormone biosynthesis            3.806996e-05
## 525   interferon gamma signaling            6.881161e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 773                0.9999996          3        6 0.04558769
## 525                0.9999925          7       72 0.04558769
## 
## $go_bp
##                                                category over_represented_pvalue
## 2914            positive regulation of defense response            1.760132e-07
## 713                       defense response to bacterium            9.279269e-07
## 4008               regulation of innate immune response            2.034887e-06
## 717                        defense response to symbiont            2.596090e-06
## 3257 positive regulation of response to biotic stimulus            6.661021e-06
## 1390                           interleukin 8 production            8.814822e-06
## 1502                                leukocyte migration            1.294731e-05
## 4734                                  response to virus            1.427926e-05
## 4362        regulation of response to cytokine stimulus            1.587860e-05
## 3037    positive regulation of interleukin 8 production            2.323508e-05
##      under_represented_pvalue numDEInCat numInCat          FDR
## 2914                1.0000000         18      329 0.0009358623
## 713                 0.9999999         11      132 0.0024668936
## 4008                0.9999996         16      309 0.0034508522
## 717                 0.9999995         14      238 0.0034508522
## 3257                0.9999987         14      265 0.0070833295
## 1390                0.9999993          7       57 0.0078114012
## 1502                0.9999975         13      236 0.0093807245
## 4734                0.9999968         15      316 0.0093807245
## 4362                0.9999977         10      139 0.0093807245
## 3037                0.9999984          6       44 0.0123435999
## 
## [1] "ExM_day_6_nor_ISL1_PTC_down"
## $reactome
##                                        category over_represented_pvalue
## 345           extracellular matrix organization            1.569637e-09
## 306                           ecm proteoglycans            9.044888e-06
## 252     degradation of the extracellular matrix            3.657581e-05
## 183                collagen chain trimerization            5.798062e-05
## 608                met activates ptk2 signaling            1.157039e-04
## 182 collagen biosynthesis and modifying enzymes            1.174285e-04
## 517          integrin cell surface interactions            1.290048e-04
## 673                          ncam1 interactions            2.322916e-04
##     under_represented_pvalue numDEInCat numInCat          FDR
## 345                1.0000000         21      230 2.079769e-06
## 306                0.9999991          8       58 5.992238e-03
## 252                0.9999941         10      106 1.615432e-02
## 183                0.9999953          6       37 1.920608e-02
## 608                0.9999924          5       27 2.441877e-02
## 182                0.9999860          7       60 2.441877e-02
## 517                0.9999844          7       63 2.441877e-02
## 673                0.9999819          5       31 3.847329e-02
## 
## $go_bp
##                                           category over_represented_pvalue
## 165                        appendage morphogenesis            9.110328e-10
## 876          embryonic skeletal system development            1.267501e-09
## 335                       cardiac cell development            8.269869e-09
## 5000            striated muscle tissue development            9.574313e-09
## 367                     cardiocyte differentiation            1.373615e-08
## 164                          appendage development            2.409646e-08
## 4552                      renal system development            2.603281e-08
## 1022 external encapsulating structure organization            2.789701e-08
## 371                          cartilage development            6.122406e-08
## 869                    embryonic organ development            6.403277e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 165                         1         16      121 3.369650e-06
## 876                         1         14       90 3.369650e-06
## 335                         1         12       69 1.272666e-05
## 5000                        1         19      199 1.272666e-05
## 367                         1         15      122 1.460702e-05
## 164                         1         16      152 1.854105e-05
## 4552                        1         22      271 1.854105e-05
## 1022                        1         21      259 1.854105e-05
## 371                         1         16      161 3.404622e-05
## 869                         1         24      347 3.404622e-05
## 
## [1] "PrS_day_6_hyp_EPAS1_CE_up"
## $reactome
##                                                                         category
## 1300                                               unfolded protein response upr
## 561                                               ire1alpha activates chaperones
## 55                                                   amino acids regulate mtorc1
## 1120                                                           signaling by vegf
## 1092                                                   signaling by interleukins
## 512  insertion of tail anchored proteins into the endoplasmic reticulum membrane
## 155                                              cellular response to starvation
## 946                                   response of eif2ak1 hri to heme deficiency
## 1005                                        ros and rns production in phagocytes
## 950                                                       response to metal ions
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1300            4.000875e-06                0.9999987         33       89
## 561             2.449957e-05                0.9999937         21       50
## 55              2.640615e-05                0.9999928         22       54
## 1120            4.249383e-05                0.9999840         33       98
## 1092            5.960855e-05                0.9999655         90      362
## 512             6.222716e-05                0.9999906         12       22
## 155             1.197661e-04                0.9999442         44      154
## 946             2.165991e-04                0.9999744          9       15
## 1005            2.351095e-04                0.9999514         13       28
## 950             2.428115e-04                0.9999827          7       10
##              FDR
## 1300 0.005301159
## 561  0.011662714
## 55   0.011662714
## 1120 0.013741832
## 1092 0.013741832
## 512  0.013741832
## 155  0.022670007
## 946  0.028767309
## 1005 0.028767309
## 950  0.028767309
## 
## $go_bp
##                                                                               category
## 4612                                          response to endoplasmic reticulum stress
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 3690                                                           regulation of autophagy
## 961                                                       er nucleus signaling pathway
## 4693                                                         response to oxygen levels
## 1578                                                                    macroautophagy
## 4722                                       response to topologically incorrect protein
## 4078                                                      regulation of macroautophagy
## 5308                                                                     wound healing
## 4364                            regulation of response to endoplasmic reticulum stress
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4612            2.242089e-12                1.0000000         82      244
## 1425            3.677141e-08                1.0000000         27       58
## 3690            4.212716e-08                1.0000000         89      328
## 961             1.263554e-07                1.0000000         22       44
## 4693            5.486186e-07                1.0000000         77      286
## 1578            7.165219e-07                1.0000000         84      324
## 4722            1.041395e-06                0.9999996         47      149
## 4078            1.120731e-06                0.9999996         48      153
## 5308            1.666703e-06                0.9999994         85      330
## 4364            1.834866e-06                0.9999995         29       76
##               FDR
## 4612 1.192118e-08
## 1425 7.466336e-05
## 3690 7.466336e-05
## 961  1.679580e-04
## 4693 5.834010e-04
## 1578 6.349578e-04
## 4722 7.448658e-04
## 4078 7.448658e-04
## 5308 9.457810e-04
## 4364 9.457810e-04
## 
## [1] "PrS_day_6_hyp_EPAS1_CE_down"
## $go_bp
##                                            category over_represented_pvalue
## 2642                  pattern specification process            1.657623e-07
## 214                                   axon guidance            1.206103e-06
## 1681                     mesenchymal cell migration            3.793624e-06
## 165                         appendage morphogenesis            1.156013e-05
## 999                establishment of tissue polarity            2.314907e-05
## 337                     cardiac chamber development            2.419292e-05
## 164                           appendage development            2.812277e-05
## 3902 regulation of establishment of planar polarity            2.882584e-05
## 2417              neural crest cell differentiation            3.806520e-05
## 2166              negative regulation of locomotion            4.169198e-05
##      under_represented_pvalue numDEInCat numInCat          FDR
## 2642                1.0000000         59      335 0.0008813579
## 214                 0.9999996         37      180 0.0032064259
## 1681                0.9999992         17       55 0.0067235658
## 165                 0.9999964         25      116 0.0153662992
## 999                 0.9999942         18       67 0.0191583720
## 337                 0.9999913         29      140 0.0191583720
## 164                 0.9999899         28      145 0.0191583720
## 3902                0.9999938         15       50 0.0191583720
## 2417                0.9999890         20       84 0.0221676277
## 2166                0.9999807         45      279 0.0221676277
## 
## [1] "PrS_day_6_hyp_EPAS1_KO_up"
## $reactome
##                         category over_represented_pvalue
## 631 metallothioneins bind metals            2.645965e-06
## 950       response to metal ions            4.355962e-06
##     under_represented_pvalue numDEInCat numInCat         FDR
## 631                1.0000000          6        7 0.002885825
## 950                0.9999998          7       10 0.002885825
## 
## $go_bp
##                                      category over_represented_pvalue
## 5308                            wound healing            1.216152e-07
## 1417       intracellular zinc ion homeostasis            1.200437e-06
## 4540              regulation of wound healing            4.743033e-06
## 486           cellular response to copper ion            1.175619e-05
## 4612 response to endoplasmic reticulum stress            1.436308e-05
## 4372       regulation of response to wounding            1.531815e-05
## 1255                               hemostasis            1.559951e-05
## 405                           cell chemotaxis            1.725306e-05
## 1497                     leukocyte chemotaxis            1.907057e-05
## 770              detoxification of copper ion            2.288500e-05
##      under_represented_pvalue numDEInCat numInCat          FDR
## 5308                1.0000000         59      325 0.0006466282
## 1417                0.9999999         12       27 0.0031913622
## 4540                0.9999987         24       97 0.0084062363
## 486                 0.9999989          9       19 0.0110996677
## 4612                0.9999938         43      244 0.0110996677
## 4372                0.9999947         28      130 0.0110996677
## 1255                0.9999941         33      166 0.0110996677
## 405                 0.9999930         37      198 0.0110996677
## 1497                0.9999932         29      141 0.0110996677
## 770                 0.9999991          6        9 0.0110996677
## 
## [1] "PrS_day_6_hyp_EPAS1_KO_down"
## $reactome
##                                    category over_represented_pvalue
## 183            collagen chain trimerization            2.838308e-05
## 252 degradation of the extracellular matrix            2.869374e-05
## 184                    collagen degradation            7.509535e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 183                0.9999964          9       36 0.01900961
## 252                0.9999930         16      105 0.01900961
## 184                0.9999874         10       49 0.03316711
## 
## $go_bp
##                                category over_represented_pvalue
## 214                       axon guidance            2.431541e-10
## 337         cardiac chamber development            6.186260e-08
## 363       cardiac ventricle development            1.431092e-07
## 869         embryonic organ development            4.013514e-07
## 5000 striated muscle tissue development            4.494209e-07
## 1701    metanephric nephron development            4.692003e-07
## 339       cardiac chamber morphogenesis            6.795407e-07
## 1681         mesenchymal cell migration            9.218570e-07
## 2642      pattern specification process            1.895457e-06
## 367          cardiocyte differentiation            2.065181e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 214                 1.0000000         31      175 1.292850e-06
## 337                 1.0000000         24      138 1.644617e-04
## 363                 1.0000000         20      103 2.536372e-04
## 869                 0.9999999         40      351 4.157896e-04
## 5000                0.9999999         28      203 4.157896e-04
## 1701                1.0000000         10       29 4.157896e-04
## 339                 0.9999999         19      104 5.161597e-04
## 1681                0.9999999         13       53 6.126892e-04
## 2642                0.9999993         37      334 1.010690e-03
## 367                 0.9999995         20      125 1.010690e-03
## 
## [1] "PrS_day_6_hyp_EPAS1_PTC_up"
## $go_bp
##                                                                       category
## 4050                                     regulation of leukocyte proliferation
## 1997                                      negative regulation of cell adhesion
## 4005                                       regulation of inflammatory response
## 477                                       cellular response to biotic stimulus
## 1504                                                   leukocyte proliferation
## 1996                                    negative regulation of cell activation
## 3657                                regulation of alpha beta t cell activation
## 98                                          amino acid transmembrane transport
## 49   adenylate cyclase activating g protein coupled receptor signaling pathway
## 1322        immune response regulating cell surface receptor signaling pathway
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4050            8.316028e-06                0.9999968         36      168
## 1997            1.423492e-05                0.9999939         43      220
## 4005            1.673653e-05                0.9999925         48      258
## 477             3.233090e-05                0.9999869         35      169
## 1504            3.764762e-05                0.9999832         42      221
## 1996            4.109780e-05                0.9999842         31      144
## 3657            4.612576e-05                0.9999867         20       76
## 98              6.389899e-05                0.9999817         19       73
## 49              7.542630e-05                0.9999757         22       89
## 1322            7.570516e-05                0.9999657         40      215
##             FDR
## 4050 0.02966271
## 1997 0.02966271
## 4005 0.02966271
## 477  0.03503581
## 1504 0.03503581
## 1996 0.03503581
## 3657 0.03503581
## 98   0.03551148
## 49   0.03551148
## 1322 0.03551148
## 
## [1] "PrS_day_6_hyp_EPAS1_PTC_down"
## $reactome
##                                                         category
## 183                                 collagen chain trimerization
## 184                                         collagen degradation
## 252                      degradation of the extracellular matrix
## 306                                            ecm proteoglycans
## 345                            extracellular matrix organization
## 517                           integrin cell surface interactions
## 182                  collagen biosynthesis and modifying enzymes
## 185                                           collagen formation
## 84  assembly of collagen fibrils and other multimeric structures
## 525                                   interferon gamma signaling
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 183            2.376243e-09                1.0000000         15       36
## 184            6.767919e-09                1.0000000         17       49
## 252            1.359401e-08                1.0000000         25      105
## 306            5.069385e-07                0.9999999         16       59
## 345            1.602928e-06                0.9999994         35      230
## 517            1.623816e-06                0.9999997         16       65
## 182            3.700694e-06                0.9999993         15       59
## 185            3.435642e-05                0.9999916         16       77
## 84             9.196376e-05                0.9999813         12       50
## 525            2.312451e-04                0.9999389         14       76
##              FDR
## 183 3.148522e-06
## 184 4.483746e-06
## 252 6.004020e-06
## 306 1.679234e-04
## 345 3.585928e-04
## 517 3.585928e-04
## 182 7.004885e-04
## 185 5.690282e-03
## 84  1.353911e-02
## 525 3.063997e-02
## 
## $go_bp
##                                   category over_represented_pvalue
## 4896         skeletal system morphogenesis            2.370129e-10
## 876  embryonic skeletal system development            6.346006e-10
## 1239                   heart morphogenesis            7.959646e-10
## 2400  negative regulation of viral process            1.241386e-09
## 870          embryonic organ morphogenesis            5.307787e-09
## 337            cardiac chamber development            7.292674e-09
## 1687                mesenchyme development            7.652884e-09
## 214                          axon guidance            8.844539e-09
## 339          cardiac chamber morphogenesis            1.550810e-08
## 363          cardiac ventricle development            1.579762e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 4896                        1         36      173 1.260197e-06
## 876                         1         24       87 1.410715e-06
## 1239                        1         40      211 1.410715e-06
## 2400                        1         22       75 1.650112e-06
## 870                         1         39      216 5.644301e-06
## 337                         1         30      138 5.812912e-06
## 1687                        1         43      257 5.812912e-06
## 214                         1         34      175 5.878302e-06
## 339                         1         25      104 8.399592e-06
## 363                         1         25      103 8.399592e-06
## 
## [1] "PrS_day_6_nor_EPAS1_CE_up"
## $go_bp
##                                          category over_represented_pvalue
## 4888         skeletal muscle cell differentiation            2.320281e-07
## 221                             b cell activation            1.222738e-06
## 360                    cardiac septum development            1.340714e-06
## 2428         neuroepithelial cell differentiation            1.418615e-06
## 1504                      leukocyte proliferation            1.959461e-06
## 488  cellular response to decreased oxygen levels            2.034921e-06
## 499               cellular response to fatty acid            2.175119e-06
## 1823             mononuclear cell differentiation            2.347164e-06
## 361                  cardiac septum morphogenesis            2.588976e-06
## 4619                       response to fatty acid            3.928866e-06
##      under_represented_pvalue numDEInCat numInCat         FDR
## 4888                1.0000000         15       55 0.001233693
## 221                 0.9999996         28      185 0.001529510
## 360                 0.9999997         19       95 0.001529510
## 2428                0.9999999         10       27 0.001529510
## 1504                0.9999994         29      203 0.001529510
## 488                 0.9999995         22      128 0.001529510
## 499                 0.9999998          9       24 0.001529510
## 1823                0.9999991         39      318 0.001529510
## 361                 0.9999995         15       64 0.001529510
## 4619                0.9999995         11       38 0.002088978
## 
## [1] "PrS_day_6_nor_EPAS1_CE_down"
## $reactome
##                                                                                           category
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 280                                                                                dna methylation
## 163                          chromatin modifications during the maternal to zygotic transition mzt
## 464                                                                     hdacs deacetylate histones
## 189                                                           condensation of prophase chromosomes
## 463                                                                               hcmv late events
## 1123                                                    sirt1 negatively regulates rrna expression
## 86                                        assembly of the orc complex at the origin of replication
## 461                                                                              hcmv early events
## 983                                                               rmts methylate histone arginines
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13              1.797855e-07                1.0000000         12       57
## 280             2.117408e-07                1.0000000         12       57
## 163             4.570043e-07                0.9999999         12       61
## 464             7.490313e-07                0.9999999         14       88
## 189             8.064858e-07                0.9999999         12       65
## 463             2.337074e-06                0.9999996         15      109
## 1123            2.659755e-06                0.9999997         11       60
## 86              3.359696e-06                0.9999996         11       61
## 461             3.672982e-06                0.9999992         16      124
## 983             3.714706e-06                0.9999994         12       72
##               FDR
## 13   0.0001400665
## 280  0.0001400665
## 163  0.0002015389
## 464  0.0002133961
## 189  0.0002133961
## 463  0.0004914556
## 1123 0.0004914556
## 86   0.0004914556
## 461  0.0004914556
## 983  0.0004914556
## 
## [1] "PrS_day_6_nor_EPAS1_PTC_up"
## $reactome
##                        category over_represented_pvalue
## 615 metabolism of carbohydrates            3.293848e-05
##     under_represented_pvalue numDEInCat numInCat       FDR
## 615                0.9999943         11      235 0.0435776
## 
## [1] "PrS_day_6_nor_FOSB_CE_up"
## $reactome
##                                                          category
## 515                            integrin cell surface interactions
## 343                             extracellular matrix organization
## 1142                                  striated muscle contraction
## 250                       degradation of the extracellular matrix
## 182                                  collagen chain trimerization
## 183                                          collagen degradation
## 84   assembly of collagen fibrils and other multimeric structures
## 181                   collagen biosynthesis and modifying enzymes
## 184                                            collagen formation
## 1160                                        syndecan interactions
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 515             5.440956e-09                1.0000000         13       62
## 343             2.703210e-08                1.0000000         23      221
## 1142            7.384844e-08                1.0000000          8       24
## 250             1.426951e-07                1.0000000         15      102
## 182             3.685600e-07                1.0000000          9       35
## 183             5.365875e-07                1.0000000         10       47
## 84              5.922329e-07                0.9999999         10       47
## 181             3.205380e-06                0.9999996         10       57
## 184             4.154909e-06                0.9999994         11       72
## 1160            5.022808e-06                0.9999997          7       26
##               FDR
## 515  7.198385e-06
## 343  1.788173e-05
## 1142 3.256716e-05
## 250  4.719639e-05
## 182  9.752097e-05
## 183  1.119320e-04
## 84   1.119320e-04
## 181  5.300897e-04
## 184  6.107716e-04
## 1160 6.645175e-04
## 
## $go_bp
##                                           category over_represented_pvalue
## 1022 external encapsulating structure organization            1.310736e-12
## 645                   collagen fibril organization            3.123706e-11
## 82                   ameboidal type cell migration            6.640154e-11
## 5000            striated muscle tissue development            7.295320e-11
## 1239                           heart morphogenesis            4.981123e-10
## 1687                        mesenchyme development            6.648361e-10
## 4997          striated muscle cell differentiation            2.878148e-09
## 5112                              tissue migration            3.005691e-09
## 1877                     muscle tissue development            6.213371e-09
## 371                          cartilage development            1.463888e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1022                        1         31      237 6.969182e-09
## 645                         1         15       54 8.304373e-08
## 82                          1         36      366 9.697305e-08
## 5000                        1         26      196 9.697305e-08
## 1239                        1         26      207 5.296926e-07
## 1687                        1         28      246 5.891556e-07
## 4997                        1         26      232 1.997658e-06
## 5112                        1         28      270 1.997658e-06
## 1877                        1         31      331 3.670721e-06
## 371                         1         20      155 7.783491e-06
## 
## [1] "PrS_day_6_nor_FOSB_KO_up"
## $reactome
##                                                         category
## 345                            extracellular matrix organization
## 517                           integrin cell surface interactions
## 306                                            ecm proteoglycans
## 252                      degradation of the extracellular matrix
## 182                  collagen biosynthesis and modifying enzymes
## 185                                           collagen formation
## 183                                 collagen chain trimerization
## 742            o glycosylation of tsr domain containing proteins
## 184                                         collagen degradation
## 84  assembly of collagen fibrils and other multimeric structures
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345            2.231190e-13                1.0000000         39      234
## 517            1.344007e-10                1.0000000         18       66
## 306            3.842552e-09                1.0000000         16       61
## 252            1.421618e-08                1.0000000         21      109
## 182            2.939011e-08                1.0000000         15       59
## 185            2.618527e-07                1.0000000         16       77
## 183            4.622359e-07                1.0000000         11       37
## 742            8.256749e-07                0.9999999         11       36
## 184            1.732608e-06                0.9999998         12       50
## 84             3.645308e-06                0.9999995         12       52
##              FDR
## 345 2.956326e-10
## 517 8.904049e-08
## 306 1.697127e-06
## 252 4.709109e-06
## 182 7.788378e-06
## 185 5.782580e-05
## 183 8.749464e-05
## 742 1.367524e-04
## 184 2.550785e-04
## 84  4.830033e-04
## 
## $go_bp
##                                           category over_represented_pvalue
## 82                   ameboidal type cell migration            7.026619e-15
## 1022 external encapsulating structure organization            2.075346e-14
## 1877                     muscle tissue development            2.842400e-14
## 5000            striated muscle tissue development            3.734463e-14
## 1239                           heart morphogenesis            4.266013e-14
## 5112                              tissue migration            5.314679e-14
## 645                   collagen fibril organization            9.202014e-13
## 917                     endothelial cell migration            1.360046e-12
## 1687                        mesenchyme development            1.757070e-12
## 659                  connective tissue development            8.410576e-12
##      under_represented_pvalue numDEInCat numInCat          FDR
## 82                          1         54      379 3.736053e-11
## 1022                        1         43      254 4.536478e-11
## 1877                        1         50      339 4.536478e-11
## 5000                        1         38      204 4.536478e-11
## 1239                        1         39      211 4.536478e-11
## 5112                        1         44      278 4.709691e-11
## 645                         1         20       60 6.989587e-10
## 917                         1         34      194 9.039206e-10
## 1687                        1         40      252 1.038038e-09
## 659                         1         36      224 4.471903e-09
## 
## [1] "PrS_day_6_nor_FOSB_PTC_up"
## $reactome
##                              category over_represented_pvalue
## 343 extracellular matrix organization            1.017386e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 343                0.9999988          9      221 0.01346002
## 
## [1] "PrS_day_6_nor_GCM1_CE_up"
## $reactome
##                                                                                           category
## 466                                                                     hdacs deacetylate histones
## 282                                                                                dna methylation
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 190                                                           condensation of prophase chromosomes
## 1125                                                    sirt1 negatively regulates rrna expression
## 606                                                                          meiotic recombination
## 827                                                               prc2 methylates histones and dna
## 164                          chromatin modifications during the maternal to zygotic transition mzt
## 86                                        assembly of the orc complex at the origin of replication
## 329                                    ercc6 csb and ehmt2 g9a positively regulate rrna expression
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 466             7.628865e-32                        1         57       89
## 282             4.165369e-31                        1         45       58
## 13              8.012020e-30                        1         44       58
## 190             9.972113e-30                        1         47       66
## 1125            1.421274e-29                        1         45       61
## 606             1.889171e-29                        1         51       77
## 827             3.455870e-28                        1         46       66
## 164             5.346084e-28                        1         45       64
## 86              1.037239e-27                        1         44       62
## 329             6.504127e-26                        1         45       69
##               FDR
## 466  1.010825e-28
## 282  2.759557e-28
## 13   3.303262e-27
## 190  3.303262e-27
## 1125 3.766375e-27
## 606  4.171919e-27
## 827  6.541468e-26
## 164  8.854451e-26
## 86   1.527047e-25
## 329  8.617968e-24
## 
## $go_bp
##                                                   category
## 2553                               nucleosome organization
## 3484   protein localization to cenp a containing chromatin
## 3450                          protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 3485                     protein localization to chromatin
## 2184  negative regulation of megakaryocyte differentiation
## 199      attachment of spindle microtubules to kinetochore
## 2592                                     organelle fission
## 4885                          sister chromatid segregation
## 1793                  mitotic sister chromatid segregation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553            1.970103e-14                1.0000000         46      115
## 3484            8.990333e-14                1.0000000         16       18
## 3450            2.710481e-11                1.0000000         59      202
## 3487            4.493061e-11                1.0000000         22       40
## 3485            3.491510e-08                1.0000000         23       55
## 2184            6.315881e-08                1.0000000         12       18
## 199             6.775164e-08                1.0000000         21       49
## 2592            2.638740e-07                1.0000000         88      424
## 4885            6.866750e-07                0.9999998         54      224
## 1793            8.266640e-07                0.9999997         47      185
##               FDR
## 2553 1.047504e-10
## 3484 2.390080e-10
## 3450 4.803876e-08
## 3487 5.972401e-08
## 3485 3.712872e-05
## 2184 5.146221e-05
## 199  5.146221e-05
## 2592 1.753773e-04
## 4885 4.056723e-04
## 1793 4.395373e-04
## 
## [1] "PrS_day_6_nor_GCM1_CE_down"
## $reactome
##                                                                      category
## 1300                                            unfolded protein response upr
## 1127                                     slc mediated transmembrane transport
## 1211                                                   thyroxine biosynthesis
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 262                     diseases associated with glycosaminoglycan metabolism
## 561                                            ire1alpha activates chaperones
## 1120                                                        signaling by vegf
## 1308                                    vegfr2 mediated vascular permeability
## 797                                              pi3k akt signaling in cancer
## 773                                              peptide hormone biosynthesis
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1300            1.373377e-05                0.9999952         34       90
## 1127            1.465164e-05                0.9999931         59      185
## 1211            4.242209e-05                1.0000000          6        6
## 1276            4.311032e-05                0.9999868         25       60
## 262             6.120233e-05                0.9999865         17       34
## 561             9.265976e-05                0.9999734         21       50
## 1120            9.552444e-05                0.9999614         35      101
## 1308            9.586607e-05                0.9999818         14       27
## 797             1.223141e-04                0.9999549         29       79
## 773             1.614522e-04                0.9999914          7        9
##              FDR
## 1300 0.009706711
## 1127 0.009706711
## 1211 0.014280293
## 1276 0.014280293
## 262  0.015877817
## 561  0.015877817
## 1120 0.015877817
## 1308 0.015877817
## 797  0.018007360
## 773  0.021392421
## 
## $go_bp
##                                                                       category
## 49   adenylate cyclase activating g protein coupled receptor signaling pathway
## 4540                                               regulation of wound healing
## 4873                                                            signal release
## 4050                                     regulation of leukocyte proliferation
## 1867                                               muscle cell differentiation
## 5308                                                             wound healing
## 5115                                                       tolerance induction
## 4679                                  response to molecule of bacterial origin
## 254                                              biomineral tissue development
## 1333                                             import across plasma membrane
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 49              2.407926e-07                0.9999999         37       90
## 4540            8.111677e-07                0.9999997         39      101
## 4873            2.561781e-06                0.9999988        105      385
## 4050            2.616669e-06                0.9999989         57      178
## 1867            3.768912e-06                0.9999983         91      325
## 5308            4.138258e-06                0.9999979         94      339
## 5115            4.829115e-06                0.9999995         13       20
## 4679            5.436606e-06                0.9999974         73      250
## 254             6.463327e-06                0.9999974         46      136
## 1333            6.829057e-06                0.9999970         52      157
##              FDR
## 49   0.001280294
## 4540 0.002156489
## 4873 0.003256707
## 4050 0.003256707
## 1867 0.003256707
## 5308 0.003256707
## 5115 0.003256707
## 4679 0.003256707
## 254  0.003256707
## 1333 0.003256707
## 
## [1] "PrS_day_6_nor_GCM1_KO_up"
## $reactome
##                                                                                           category
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 282                                                                                dna methylation
## 190                                                           condensation of prophase chromosomes
## 1125                                                    sirt1 negatively regulates rrna expression
## 466                                                                     hdacs deacetylate histones
## 827                                                               prc2 methylates histones and dna
## 86                                        assembly of the orc complex at the origin of replication
## 606                                                                          meiotic recombination
## 164                          chromatin modifications during the maternal to zygotic transition mzt
## 757                                                            oxidative stress induced senescence
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13              2.074386e-31                        1         43       58
## 282             2.785576e-31                        1         43       58
## 190             2.931739e-30                        1         45       66
## 1125            6.939695e-30                        1         43       61
## 466             9.213743e-30                        1         52       89
## 827             1.117953e-28                        1         44       66
## 86              4.714334e-28                        1         42       62
## 606             3.173461e-27                        1         46       76
## 164             3.802281e-27                        1         42       64
## 757             1.600800e-25                        1         56      116
##               FDR
## 13   1.845444e-28
## 282  1.845444e-28
## 190  1.294851e-27
## 1125 2.298774e-27
## 466  2.441642e-27
## 827  2.468813e-26
## 86   8.923562e-26
## 606  5.256045e-25
## 164  5.597802e-25
## 757  2.121060e-23
## 
## $go_bp
##                                                   category
## 2553                               nucleosome organization
## 3484   protein localization to cenp a containing chromatin
## 3487 protein localization to chromosome centromeric region
## 3450                          protein dna complex assembly
## 2184  negative regulation of megakaryocyte differentiation
## 3485                     protein localization to chromatin
## 2592                                     organelle fission
## 4090           regulation of megakaryocyte differentiation
## 3486                    protein localization to chromosome
## 4161            regulation of myeloid cell differentiation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553            1.979412e-17                1.0000000         46      115
## 3484            4.618459e-15                1.0000000         16       18
## 3487            1.151894e-12                1.0000000         22       40
## 3450            2.203885e-12                1.0000000         55      202
## 2184            7.868912e-09                1.0000000         12       18
## 3485            4.096094e-08                1.0000000         21       55
## 2592            2.629131e-07                1.0000000         77      423
## 4090            2.877743e-07                1.0000000         15       34
## 3486            8.745217e-07                0.9999997         30      114
## 4161            2.558540e-06                0.9999991         37      161
##               FDR
## 2553 1.052453e-13
## 3484 1.227817e-11
## 3487 2.041540e-09
## 3450 2.929514e-09
## 2184 8.367801e-06
## 3485 3.629822e-05
## 2592 1.912620e-04
## 4090 1.912620e-04
## 3486 5.166480e-04
## 4161 1.360376e-03
## 
## [1] "PrS_day_6_nor_GCM1_KO_down"
## $reactome
##                                                                      category
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 345                                         extracellular matrix organization
## 773                                              peptide hormone biosynthesis
## 1324                                                        zinc transporters
## 629                                                metal ion slc transporters
## 1127                                     slc mediated transmembrane transport
## 269                                                 diseases of glycosylation
## 262                     diseases associated with glycosaminoglycan metabolism
## 665                                                        muscle contraction
## 92                                                       attachment and entry
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1276            9.033249e-06                0.9999976         24       61
## 345             2.761870e-05                0.9999862         63      243
## 773             4.537917e-05                0.9999981          7        9
## 1324            4.851570e-05                0.9999957          9       14
## 629             4.872277e-05                0.9999927         12       23
## 1127            6.110895e-05                0.9999708         50      185
## 269             9.593785e-05                0.9999587         38      129
## 262             1.229663e-04                0.9999726         15       34
## 665             1.284997e-04                0.9999403         43      155
## 92              1.581947e-04                0.9999784         10       18
##             FDR
## 1276 0.01196906
## 345  0.01291154
## 773  0.01291154
## 1324 0.01291154
## 629  0.01291154
## 1127 0.01349489
## 269  0.01815966
## 262  0.01891801
## 665  0.01891801
## 92   0.02096080
## 
## $go_bp
##                                            category over_represented_pvalue
## 4540                    regulation of wound healing            4.121137e-07
## 4050          regulation of leukocyte proliferation            1.340747e-06
## 1333                  import across plasma membrane            2.917310e-06
## 1900                        myotube differentiation            3.820701e-06
## 4269 regulation of polysaccharide metabolic process            4.871069e-06
## 5308                                  wound healing            5.041807e-06
## 5076                                          taxis            6.077965e-06
## 1867                    muscle cell differentiation            7.149419e-06
## 1502                            leukocyte migration            8.383686e-06
## 1504                        leukocyte proliferation            9.701875e-06
##      under_represented_pvalue numDEInCat numInCat         FDR
## 4540                0.9999999         36      102 0.002191209
## 4050                0.9999995         51      176 0.003564376
## 1333                0.9999988         47      156 0.004467882
## 1900                0.9999987         33       98 0.004467882
## 4269                0.9999991         17       36 0.004467882
## 5308                0.9999977         82      338 0.004467882
## 5076                0.9999970         79      325 0.004616649
## 1867                0.9999965         79      324 0.004751683
## 1502                0.9999960         68      271 0.004952896
## 1504                0.9999956         60      232 0.005158487
## 
## [1] "PrS_day_6_nor_GCM1_PTC_up"
## $reactome
##                                                                                           category
## 282                                                                                dna methylation
## 466                                                                     hdacs deacetylate histones
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 190                                                           condensation of prophase chromosomes
## 827                                                               prc2 methylates histones and dna
## 1125                                                    sirt1 negatively regulates rrna expression
## 86                                        assembly of the orc complex at the origin of replication
## 164                          chromatin modifications during the maternal to zygotic transition mzt
## 606                                                                          meiotic recombination
## 757                                                            oxidative stress induced senescence
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 282             1.167401e-26                        1         38       58
## 466             7.813261e-26                        1         46       89
## 13              1.698567e-25                        1         37       58
## 190             4.538252e-25                        1         39       66
## 827             9.147834e-25                        1         39       66
## 1125            2.293100e-24                        1         37       61
## 86              6.179870e-24                        1         37       62
## 164             3.066340e-23                        1         37       64
## 606             1.649465e-22                        1         40       77
## 757             2.146886e-22                        1         50      117
##               FDR
## 282  1.546806e-23
## 466  5.176285e-23
## 13   7.502005e-23
## 190  1.503296e-22
## 827  2.424176e-22
## 1125 5.063930e-22
## 86   1.169761e-21
## 164  5.078625e-21
## 606  2.428378e-20
## 757  2.844624e-20
## 
## $go_bp
##                                                   category
## 3484   protein localization to cenp a containing chromatin
## 2553                               nucleosome organization
## 3450                          protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 2184  negative regulation of megakaryocyte differentiation
## 3485                     protein localization to chromatin
## 4090           regulation of megakaryocyte differentiation
## 4161            regulation of myeloid cell differentiation
## 2592                                     organelle fission
## 2213   negative regulation of myeloid cell differentiation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3484            6.242761e-16                1.0000000         16       18
## 2553            2.067844e-15                1.0000000         41      115
## 3450            1.240006e-11                1.0000000         50      202
## 3487            1.358815e-11                1.0000000         20       40
## 2184            1.935383e-09                1.0000000         12       18
## 3485            3.010988e-08                1.0000000         20       55
## 4090            6.273259e-08                1.0000000         15       34
## 4161            2.225727e-07                0.9999999         37      163
## 2592            4.715835e-06                0.9999978         68      426
## 2213            6.729962e-06                0.9999983         20       74
##               FDR
## 3484 3.319276e-12
## 2553 5.497363e-12
## 3450 1.806204e-08
## 3487 1.806204e-08
## 2184 2.058086e-06
## 3485 2.668237e-05
## 4090 4.764989e-05
## 4161 1.479274e-04
## 2592 2.786011e-03
## 2213 3.578321e-03
## 
## [1] "PrS_day_6_nor_GCM1_PTC_down"
## $reactome
##                                                                      category
## 345                                         extracellular matrix organization
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 269                                                 diseases of glycosylation
## 773                                              peptide hormone biosynthesis
## 1127                                     slc mediated transmembrane transport
## 665                                                        muscle contraction
## 1300                                            unfolded protein response upr
## 774                                                peptide hormone metabolism
## 629                                                metal ion slc transporters
## 271                                                    diseases of metabolism
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345             2.538992e-05                0.9999874         63      240
## 1276            3.567279e-05                0.9999896         23       61
## 269             5.075084e-05                0.9999787         39      129
## 773             5.139355e-05                0.9999978          7        9
## 1127            9.085653e-05                0.9999558         50      186
## 665             1.263344e-04                0.9999409         44      158
## 1300            1.709589e-04                0.9999349         28       90
## 774             1.871275e-04                0.9999386         22       64
## 629             3.157434e-04                0.9999430         11       23
## 271             3.313700e-04                0.9998235         54      214
##             FDR
## 345  0.01702411
## 1276 0.01702411
## 269  0.01702411
## 773  0.01702411
## 1127 0.02407698
## 665  0.02789886
## 1300 0.03099299
## 774  0.03099299
## 629  0.04390652
## 271  0.04390652
## 
## $go_bp
##                                                              category
## 5308                                                    wound healing
## 254                                     biomineral tissue development
## 4873                                                   signal release
## 4540                                      regulation of wound healing
## 560  cellular response to vascular endothelial growth factor stimulus
## 4050                            regulation of leukocyte proliferation
## 1333                                    import across plasma membrane
## 1299                                                hormone transport
## 1687                                           mesenchyme development
## 405                                                   cell chemotaxis
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5308            3.459466e-07                1.0000000         86      341
## 254             3.980891e-07                0.9999999         44      136
## 4873            4.399594e-07                1.0000000         94      384
## 4540            5.513155e-07                0.9999998         36      103
## 560             1.034616e-06                0.9999998         24       57
## 4050            2.115641e-06                0.9999991         51      178
## 1333            3.956322e-06                0.9999984         47      157
## 1299            4.151735e-06                0.9999983         64      246
## 1687            4.340907e-06                0.9999980         67      257
## 405             4.507151e-06                0.9999980         57      211
##               FDR
## 5308 0.0007328362
## 254  0.0007328362
## 4873 0.0007328362
## 4540 0.0007328362
## 560  0.0011002107
## 4050 0.0018748107
## 1333 0.0023410892
## 1299 0.0023410892
## 1687 0.0023410892
## 405  0.0023410892
## 
## [1] "PrS_day_6_nor_GRHL1_CE_up"
## $reactome
##                            category over_represented_pvalue
## 524 interferon alpha beta signaling            1.699588e-07
##     under_represented_pvalue numDEInCat numInCat          FDR
## 524                        1         19       62 0.0002251954
## 
## $go_bp
##                                  category over_represented_pvalue
## 4644          response to interferon beta            8.544205e-09
## 513  cellular response to interferon beta            3.839167e-08
## 1877            muscle tissue development            3.931756e-08
## 5000   striated muscle tissue development            6.105285e-08
## 1687               mesenchyme development            1.338063e-07
## 1239                  heart morphogenesis            2.906312e-07
## 1680     mesenchymal cell differentiation            3.613632e-07
## 4901     smad protein signal transduction            1.320695e-06
## 4727        response to type i interferon            1.588718e-06
## 2642        pattern specification process            1.661192e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 4644                1.0000000         13       26 4.542954e-05
## 513                 1.0000000         11       20 6.968382e-05
## 1877                1.0000000         59      346 6.968382e-05
## 5000                1.0000000         42      209 8.115451e-05
## 1687                1.0000000         47      257 1.422896e-04
## 1239                0.9999999         42      217 2.575477e-04
## 1680                0.9999999         41      215 2.744812e-04
## 4901                0.9999997         19       66 8.777666e-04
## 4727                0.9999997         19       68 8.832560e-04
## 2642                0.9999993         54      334 8.832560e-04
## 
## [1] "PrS_day_6_nor_GRHL1_CE_down"
## $go_bp
##                                                                       category
## 1299                                                         hormone transport
## 477                                       cellular response to biotic stimulus
## 885                                                endocrine hormone secretion
## 887                                                          endocrine process
## 2000                                 negative regulation of cell cell adhesion
## 49   adenylate cyclase activating g protein coupled receptor signaling pathway
## 1939                       negative regulation of alpha beta t cell activation
## 1941                    negative regulation of alpha beta t cell proliferation
## 4679                                  response to molecule of bacterial origin
## 3216                          positive regulation of protein catabolic process
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1299            9.898823e-08                1.0000000         58      247
## 477             3.375355e-07                0.9999999         46      181
## 885             6.847593e-07                0.9999999         19       47
## 887             9.861500e-07                0.9999998         24       70
## 2000            1.036133e-06                0.9999996         38      143
## 49              1.410249e-06                0.9999996         28       91
## 1939            1.817206e-06                0.9999997         15       33
## 1941            4.266746e-06                0.9999998          8       11
## 4679            5.331365e-06                0.9999977         55      254
## 3216            5.703751e-06                0.9999976         45      195
##               FDR
## 1299 0.0005263204
## 477  0.0008973382
## 885  0.0011018235
## 887  0.0011018235
## 2000 0.0011018235
## 49   0.0012497160
## 1939 0.0013802975
## 1941 0.0028357861
## 4679 0.0030326846
## 3216 0.0030326846
## 
## [1] "PrS_day_6_nor_GRHL1_KO_up"
## $reactome
##                                        category over_represented_pvalue
## 524             interferon alpha beta signaling            7.673542e-09
## 345           extracellular matrix organization            6.291363e-07
## 252     degradation of the extracellular matrix            5.661167e-06
## 306                           ecm proteoglycans            8.504193e-06
## 525                  interferon gamma signaling            1.720475e-05
## 183                collagen chain trimerization            3.180028e-05
## 517          integrin cell surface interactions            9.363410e-05
## 665                          muscle contraction            9.469591e-05
## 182 collagen biosynthesis and modifying enzymes            1.469891e-04
## 184                        collagen degradation            1.598360e-04
##     under_represented_pvalue numDEInCat numInCat          FDR
## 524                1.0000000         19       62 1.016744e-05
## 345                0.9999998         38      243 4.168028e-04
## 252                0.9999984         22      112 2.500349e-03
## 306                0.9999983         15       62 2.817014e-03
## 525                0.9999961         16       77 4.559258e-03
## 183                0.9999949         11       38 7.022562e-03
## 517                0.9999776         14       68 1.568401e-02
## 665                0.9999654         25      158 1.568401e-02
## 182                0.9999657         13       60 2.117827e-02
## 184                0.9999652         12       52 2.117827e-02
## 
## $go_bp
##                                             category over_represented_pvalue
## 1877                       muscle tissue development            1.741141e-09
## 5000              striated muscle tissue development            8.004665e-09
## 1451                   kidney epithelium development            2.270402e-08
## 2397 negative regulation of viral genome replication            7.586162e-08
## 2409                             nephron development            2.104257e-07
## 1687                          mesenchyme development            1.028779e-06
## 2610                                    ossification            1.302951e-06
## 2400            negative regulation of viral process            1.309864e-06
## 4552                        renal system development            1.626193e-06
## 1696                         mesonephros development            1.786292e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1877                1.0000000         54      345 9.257648e-06
## 5000                1.0000000         38      207 2.128040e-05
## 1451                1.0000000         27      122 4.023910e-05
## 2397                1.0000000         16       49 1.008391e-04
## 2409                0.9999999         26      127 2.237666e-04
## 1687                0.9999996         39      256 8.705681e-04
## 2610                0.9999995         48      348 8.705681e-04
## 2400                0.9999997         18       74 8.705681e-04
## 4552                0.9999994         41      274 9.471533e-04
## 1696                0.9999996         19       82 9.471533e-04
## 
## [1] "PrS_day_6_nor_GRHL1_KO_down"
## $go_bp
##                                         category over_represented_pvalue
## 3261 positive regulation of response to wounding            2.585208e-06
## 3372        positive regulation of wound healing            3.223483e-06
## 4679    response to molecule of bacterial origin            1.224157e-05
## 1299                           hormone transport            1.356104e-05
## 4873                              signal release            2.770920e-05
## 1295                hormone biosynthetic process            5.226929e-05
## 295     c21 steroid hormone biosynthetic process            6.297194e-05
## 477         cellular response to biotic stimulus            7.672578e-05
## 1298                   hormone metabolic process            7.980428e-05
##      under_represented_pvalue numDEInCat numInCat         FDR
## 3261                0.9999995         17       62 0.008569629
## 3372                0.9999994         15       50 0.008569629
## 4679                0.9999949         39      254 0.018026010
## 1299                0.9999944         38      247 0.018026010
## 4873                0.9999866         52      386 0.029465968
## 1295                0.9999892         13       51 0.046319300
## 295                 0.9999946          7       16 0.047146593
## 477                 0.9999698         29      181 0.047146593
## 1298                0.9999691         28      175 0.047146593
## 
## [1] "PrS_day_6_nor_GRHL1_PTC_up"
## $reactome
##                                    category over_represented_pvalue
## 517      integrin cell surface interactions            1.267443e-08
## 345       extracellular matrix organization            2.549363e-08
## 709  non integrin membrane ecm interactions            8.874315e-08
## 282                         dna methylation            4.656990e-07
## 306                       ecm proteoglycans            7.256488e-07
## 957                    rho gtpase effectors            1.287106e-06
## 985        rmts methylate histone arginines            3.665050e-06
## 190    condensation of prophase chromosomes            4.636888e-06
## 183            collagen chain trimerization            4.682617e-06
## 252 degradation of the extracellular matrix            6.161534e-06
##     under_represented_pvalue numDEInCat numInCat          FDR
## 517                1.0000000         28       68 1.679363e-05
## 345                1.0000000         65      243 1.688953e-05
## 709                1.0000000         24       56 3.919489e-05
## 282                0.9999999         22       58 1.542628e-04
## 306                0.9999998         24       62 1.922969e-04
## 957                0.9999996         67      298 2.842359e-04
## 985                0.9999990         24       73 6.893852e-04
## 190                0.9999988         22       66 6.893852e-04
## 183                0.9999991         17       38 6.893852e-04
## 252                0.9999978         34      112 7.476358e-04
## 
## $go_bp
##                                                       category
## 82                               ameboidal type cell migration
## 18                                 actin filament organization
## 38                           actomyosin structure organization
## 4552                                  renal system development
## 2642                             pattern specification process
## 1877                                 muscle tissue development
## 5112                                          tissue migration
## 1239                                       heart morphogenesis
## 398  cell cell adhesion via plasma membrane adhesion molecules
## 5308                                             wound healing
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 82              5.169906e-10                        1         97      382
## 18              1.262618e-09                        1        102      417
## 38              4.850766e-09                        1         56      185
## 4552            1.007518e-08                        1         74      273
## 2642            1.121394e-08                        1         85      334
## 1877            2.570479e-08                        1         85      343
## 5112            4.767414e-08                        1         72      281
## 1239            5.525425e-08                        1         61      218
## 398             7.978064e-08                        1         64      219
## 5308            8.907983e-08                        1         83      345
##               FDR
## 82   2.748839e-06
## 18   3.356669e-06
## 38   8.597175e-06
## 4552 1.192490e-05
## 2642 1.192490e-05
## 1877 2.277873e-05
## 5112 3.621191e-05
## 1239 3.672336e-05
## 398  4.713263e-05
## 5308 4.736375e-05
## 
## [1] "PrS_day_6_nor_GRHL1_PTC_down"
## $reactome
##                                        category over_represented_pvalue
## 1300              unfolded protein response upr            1.276041e-06
## 90    atf6 atf6 alpha activates chaperone genes            1.347247e-05
## 79            asparagine n linked glycosylation            3.650391e-05
## 91         atf6 atf6 alpha activates chaperones            1.089538e-04
## 946  response of eif2ak1 hri to heme deficiency            1.306559e-04
## 561              ire1alpha activates chaperones            1.312578e-04
##      under_represented_pvalue numDEInCat numInCat         FDR
## 1300                0.9999996         33       90 0.001690754
## 90                  0.9999994          8       10 0.008925511
## 79                  0.9999807         71      283 0.016122558
## 91                  0.9999911          8       12 0.028986103
## 946                 0.9999856          9       15 0.028986103
## 561                 0.9999629         19       50 0.028986103
## 
## $go_bp
##                                                    category
## 1299                                      hormone transport
## 4612               response to endoplasmic reticulum stress
## 887                                       endocrine process
## 3494          protein localization to endoplasmic reticulum
## 4679               response to molecule of bacterial origin
## 477                    cellular response to biotic stimulus
## 1939    negative regulation of alpha beta t cell activation
## 885                             endocrine hormone secretion
## 3657             regulation of alpha beta t cell activation
## 1941 negative regulation of alpha beta t cell proliferation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1299            2.888093e-08                1.0000000         72      249
## 4612            1.589375e-07                1.0000000         69      245
## 887             4.843992e-07                0.9999999         28       69
## 3494            1.268246e-06                0.9999997         27       68
## 4679            2.734772e-06                0.9999988         68      255
## 477             4.396961e-06                0.9999981         52      181
## 1939            4.776631e-06                0.9999991         17       35
## 885             5.917315e-06                0.9999987         20       46
## 3657            6.241900e-06                0.9999981         29       81
## 1941            7.518669e-06                0.9999996          9       12
##               FDR
## 1299 0.0001535599
## 4612 0.0004225354
## 887  0.0008585168
## 3494 0.0016858155
## 4679 0.0029081562
## 477  0.0036281926
## 1939 0.0036281926
## 885  0.0036875758
## 3657 0.0036875758
## 1941 0.0039976765
## 
## [1] "PrS_day_6_nor_POU2F3_CE_up"
## $reactome
##                                category over_represented_pvalue
## 517  integrin cell surface interactions            1.037525e-06
## 149          cell junction organization            6.662492e-06
## 144             cell cell communication            9.679569e-06
## 40      adherens junctions interactions            2.153966e-05
## 145     cell cell junction organization            2.232466e-05
## 466          hdacs deacetylate histones            4.919255e-05
## 631        metallothioneins bind metals            7.636329e-05
## 345   extracellular matrix organization            9.947772e-05
## 463                   hcmv early events            1.345601e-04
## 173 class b 2 secretin family receptors            1.558919e-04
##     under_represented_pvalue numDEInCat numInCat         FDR
## 517                0.9999998         16       65 0.001374720
## 149                0.9999984         19       96 0.004275143
## 144                0.9999972         22      126 0.004275143
## 40                 0.9999963         12       46 0.005916035
## 145                0.9999951         15       70 0.005916035
## 466                0.9999881         15       89 0.010863354
## 631                0.9999985          4        6 0.014454480
## 345                0.9999595         30      233 0.016475997
## 463                0.9999585         18      126 0.019810236
## 173                0.9999659         12       56 0.020619466
## 
## $go_bp
##                                  category over_represented_pvalue
## 5112                     tissue migration            4.906286e-10
## 1687               mesenchyme development            5.442005e-10
## 82          ameboidal type cell migration            1.759847e-09
## 1680     mesenchymal cell differentiation            1.662299e-08
## 38      actomyosin structure organization            2.025864e-08
## 18            actin filament organization            1.163100e-07
## 954  epithelial to mesenchymal transition            1.582246e-07
## 4548                     renal filtration            2.247731e-07
## 4970               sprouting angiogenesis            4.621466e-07
## 428                  cell matrix adhesion            7.251283e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 5112                1.0000000         46      278 1.446757e-06
## 1687                1.0000000         44      252 1.446757e-06
## 82                  1.0000000         55      379 3.119035e-06
## 1680                1.0000000         37      212 2.154303e-05
## 38                  1.0000000         33      182 2.154303e-05
## 18                  1.0000000         53      407 1.030701e-04
## 954                 1.0000000         28      148 1.201829e-04
## 4548                1.0000000         10       21 1.493898e-04
## 4970                0.9999999         22      106 2.730259e-04
## 428                 0.9999998         32      194 3.713563e-04
## 
## [1] "PrS_day_6_nor_POU2F3_CE_down"
## $go_bp
##                                                              category
## 1900                                          myotube differentiation
## 418                                              cell fate commitment
## 3206     positive regulation of potassium ion transmembrane transport
## 498                       cellular response to extracellular stimulus
## 4697                                      response to peptide hormone
## 4168                            regulation of myotube differentiation
## 295                          c21 steroid hormone biosynthetic process
## 560  cellular response to vascular endothelial growth factor stimulus
## 1295                                     hormone biosynthetic process
## 3735                     regulation of carbohydrate metabolic process
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1900            4.319177e-06                0.9999989         20       98
## 418             7.666638e-06                0.9999974         29      182
## 3206            1.918990e-05                0.9999983          8       20
## 498             3.175180e-05                0.9999870         34      247
## 4697            3.306172e-05                0.9999849         43      343
## 4168            3.329037e-05                0.9999952         10       33
## 295             3.395144e-05                0.9999974          7       16
## 560             4.253434e-05                0.9999913         13       55
## 1295            4.645070e-05                0.9999912         12       48
## 3735            4.881880e-05                0.9999832         24      151
##             FDR
## 1900 0.02038176
## 418  0.02038176
## 3206 0.02135903
## 498  0.02135903
## 4697 0.02135903
## 4168 0.02135903
## 295  0.02135903
## 560  0.02135903
## 1295 0.02135903
## 3735 0.02135903
## 
## [1] "PrS_day_6_nor_POU2F3_KO_up"
## $reactome
##                                                                                           category
## 464                                                                     hdacs deacetylate histones
## 461                                                                              hcmv early events
## 463                                                                               hcmv late events
## 983                                                               rmts methylate histone arginines
## 825                                                               prc2 methylates histones and dna
## 462                                                                                 hcmv infection
## 280                                                                                dna methylation
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 1123                                                    sirt1 negatively regulates rrna expression
## 271                                                              diseases of programmed cell death
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 464             1.356736e-08                1.0000000         13       88
## 461             1.181835e-06                0.9999998         13      124
## 463             1.321121e-06                0.9999998         12      109
## 983             1.487783e-06                0.9999998         10       72
## 825             5.011437e-06                0.9999995          9       65
## 462             7.928422e-06                0.9999986         13      147
## 280             1.218431e-05                0.9999988          8       56
## 13              1.268151e-05                0.9999987          8       57
## 1123            1.765808e-05                0.9999981          8       60
## 271             1.971687e-05                0.9999971         10       94
##               FDR
## 464  1.794961e-05
## 461  4.920841e-04
## 463  4.920841e-04
## 983  4.920841e-04
## 825  1.326026e-03
## 462  1.748217e-03
## 280  2.097205e-03
## 13   2.097205e-03
## 1123 2.391517e-03
## 271  2.391517e-03
## 
## $go_bp
##                                                       category
## 82                               ameboidal type cell migration
## 4901                          smad protein signal transduction
## 5112                                          tissue migration
## 1875                                muscle organ morphogenesis
## 1687                                    mesenchyme development
## 403                                 cell cell signaling by wnt
## 398  cell cell adhesion via plasma membrane adhesion molecules
## 425                                  cell junction disassembly
## 1680                          mesenchymal cell differentiation
## 4399            regulation of smad protein signal transduction
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 82              4.252388e-08                1.0000000         27      353
## 4901            7.673828e-07                0.9999999         10       58
## 5112            2.282230e-06                0.9999994         20      260
## 1875            6.725705e-06                0.9999993          9       56
## 1687            1.221280e-05                0.9999968         18      238
## 403             1.401595e-05                0.9999956         23      369
## 398             4.106912e-05                0.9999899         15      170
## 425             4.779874e-05                0.9999976          5       17
## 1680            6.849303e-05                0.9999823         15      200
## 4399            7.701841e-05                0.9999935          6       32
##               FDR
## 82   0.0002260995
## 4901 0.0020400872
## 5112 0.0040448716
## 1875 0.0089401433
## 1687 0.0124204674
## 403  0.0124204674
## 398  0.0311949287
## 425  0.0317682382
## 1680 0.0404641628
## 4399 0.0409506872
## 
## [1] "PrS_day_6_nor_PPARG_CE_up"
## $reactome
##                               category over_represented_pvalue
## 456                gpcr ligand binding            7.898034e-06
## 144            cell cell communication            1.457879e-05
## 517 integrin cell surface interactions            3.829954e-05
## 123                        ca2 pathway            1.343681e-04
## 550           intraflagellar transport            1.838278e-04
## 40     adherens junctions interactions            2.060363e-04
## 149         cell junction organization            2.538944e-04
##     under_represented_pvalue numDEInCat numInCat         FDR
## 456                0.9999966         50      229 0.009658448
## 144                0.9999947         32      127 0.009658448
## 517                0.9999893         20       69 0.016915630
## 123                0.9999632         17       56 0.044509419
## 550                0.9999530         15       49 0.045499673
## 40                 0.9999471         15       47 0.045499673
## 149                0.9999059         24       97 0.048058576
## 
## $go_bp
##                                                             category
## 398        cell cell adhesion via plasma membrane adhesion molecules
## 1239                                             heart morphogenesis
## 18                                       actin filament organization
## 3641                      regulation of actin filament based process
## 1293 homophilic cell adhesion via plasma membrane adhesion molecules
## 38                                 actomyosin structure organization
## 1877                                       muscle tissue development
## 339                                    cardiac chamber morphogenesis
## 371                                            cartilage development
## 363                                    cardiac ventricle development
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 398             3.661748e-09                1.0000000         63      221
## 1239            1.239773e-08                1.0000000         57      216
## 18              6.666190e-08                1.0000000         87      420
## 3641            1.199304e-07                1.0000000         73      337
## 1293            1.533619e-07                0.9999999         45      143
## 38              1.676905e-07                0.9999999         48      187
## 1877            2.783577e-07                1.0000000         74      345
## 339             4.279965e-07                0.9999999         33      106
## 371             4.567058e-07                0.9999998         43      164
## 363             7.066016e-07                0.9999998         33      106
##               FDR
## 398  1.946951e-05
## 1239 3.295937e-05
## 18   1.181471e-04
## 3641 1.486018e-04
## 1293 1.486018e-04
## 38   1.486018e-04
## 1877 2.114325e-04
## 339  2.698116e-04
## 371  2.698116e-04
## 363  3.375820e-04
## 
## [1] "PrS_day_6_nor_PPARG_CE_down"
## $reactome
##                                                                      category
## 1127                                     slc mediated transmembrane transport
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 946                                response of eif2ak1 hri to heme deficiency
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1127            6.654879e-06                0.9999971         51      187
## 1276            3.187680e-05                0.9999909         22       61
## 946             7.816864e-05                0.9999920          9       15
##              FDR
## 1127 0.008817715
## 1276 0.021118378
## 946  0.034524481
## 
## $go_bp
##                                            category over_represented_pvalue
## 2601                        organic anion transport            5.947848e-08
## 4891              skeletal muscle organ development            1.786796e-07
## 4740                response to xenobiotic stimulus            4.540260e-07
## 3715                regulation of body fluid levels            7.387445e-07
## 3063 positive regulation of lipid catabolic process            9.376836e-07
## 5241                             vascular transport            2.352882e-06
## 4056               regulation of lipid localization            2.953541e-06
## 4926             sodium ion transmembrane transport            3.421155e-06
## 3066 positive regulation of lipid metabolic process            4.116979e-06
## 1504                        leukocyte proliferation            6.037574e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 2601                1.0000000         81      323 0.0003162471
## 4891                0.9999999         44      142 0.0004750196
## 4740                1.0000000         77      317 0.0008046854
## 3715                1.0000000         69      278 0.0009819761
## 3063                0.9999999         11       16 0.0009971327
## 5241                0.9999993         27       76 0.0020850453
## 4056                0.9999989         39      131 0.0022434254
## 4926                0.9999988         37      123 0.0022737849
## 3066                0.9999986         34      109 0.0024322199
## 1504                0.9999973         60      241 0.0032101783
## 
## [1] "PrS_day_6_nor_PPARG_KO_up"
## $reactome
##                               category over_represented_pvalue
## 665                 muscle contraction            9.619196e-06
## 456                gpcr ligand binding            9.879185e-05
## 123                        ca2 pathway            1.104773e-04
## 517 integrin cell surface interactions            1.615082e-04
## 183       collagen chain trimerization            1.743985e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 665                0.9999966         30      157 0.01274543
## 456                0.9999565         36      229 0.04621560
## 123                0.9999738         14       56 0.04621560
## 517                0.9999572         15       68 0.04621560
## 183                0.9999659         11       38 0.04621560
## 
## $go_bp
##                                               category over_represented_pvalue
## 3179 positive regulation of osteoblast differentiation            1.557278e-09
## 869                        embryonic organ development            4.500513e-09
## 870                      embryonic organ morphogenesis            7.967119e-09
## 371                              cartilage development            7.994094e-09
## 2642                     pattern specification process            8.981302e-09
## 4896                     skeletal system morphogenesis            9.153282e-09
## 2610                                      ossification            9.462909e-09
## 2612                        osteoblast differentiation            2.995318e-08
## 4230          regulation of osteoblast differentiation            4.560799e-08
## 18                         actin filament organization            8.540476e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 3179                        1         22       62 7.187755e-06
## 869                         1         63      357 7.187755e-06
## 870                         1         45      218 7.187755e-06
## 371                         1         37      164 7.187755e-06
## 2642                        1         59      331 7.187755e-06
## 4896                        1         38      172 7.187755e-06
## 2610                        1         61      350 7.187755e-06
## 2612                        1         41      198 1.990763e-05
## 4230                        1         28      109 2.694419e-05
## 18                          1         65      417 4.540971e-05
## 
## [1] "PrS_day_6_nor_PPARG_KO_down"
## $reactome
##                                            category over_represented_pvalue
## 150  cell surface interactions at the vascular wall            3.270906e-06
## 773                    peptide hormone biosynthesis            8.657772e-05
## 1127           slc mediated transmembrane transport            9.334116e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 150                 0.9999991         26       95 0.00433395
## 773                 0.9999957          6        9 0.04122568
## 1127                0.9999589         37      186 0.04122568
## 
## $go_bp
##                                            category over_represented_pvalue
## 3063 positive regulation of lipid catabolic process            2.541265e-08
## 3066 positive regulation of lipid metabolic process            3.765024e-08
## 4056               regulation of lipid localization            1.272134e-07
## 456               cellular ketone metabolic process            3.595200e-07
## 2601                        organic anion transport            6.009201e-07
## 4923       sodium ion export across plasma membrane            7.155889e-07
## 1414           intracellular sodium ion homeostasis            1.222689e-06
## 4926             sodium ion transmembrane transport            1.539856e-06
## 3065      positive regulation of lipid localization            1.769716e-06
## 1514                        lipid catabolic process            4.396169e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 3063                1.0000000         11       16 0.0001000932
## 3066                1.0000000         31      108 0.0001000932
## 4056                1.0000000         34      131 0.0002254645
## 456                 0.9999999         40      174 0.0004778919
## 2601                1.0000000         60      320 0.0006341311
## 4923                1.0000000          7        8 0.0006341311
## 1414                0.9999999          9       14 0.0009287196
## 4926                0.9999995         30      120 0.0010234269
## 3065                0.9999995         24       85 0.0010455087
## 1514                0.9999981         50      261 0.0022499372
## 
## [1] "PrS_day_6_nor_PPARG_PTC_up"
## $reactome
##                                                             category
## 146                                           cell cycle checkpoints
## 254 deposition of new cenpa containing nucleosomes at the centromere
## 943                          resolution of sister chromatid cohesion
## 957                                             rho gtpase effectors
## 653                                       mitotic spindle checkpoint
## 959                                     rho gtpases activate formins
## 190                             condensation of prophase chromosomes
## 273                                diseases of programmed cell death
## 592                                                          m phase
## 282                                                  dna methylation
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 146            8.790600e-11                1.0000000         62      282
## 254            2.288581e-10                1.0000000         25       67
## 943            6.878032e-10                1.0000000         35      118
## 957            3.394532e-09                1.0000000         61      298
## 653            4.599742e-09                1.0000000         32      110
## 959            5.187457e-09                1.0000000         36      132
## 190            1.598867e-07                1.0000000         21       66
## 273            1.798575e-07                1.0000000         27       98
## 592            2.559695e-07                1.0000000         69      398
## 282            4.533029e-07                0.9999999         19       58
##              FDR
## 146 1.164755e-07
## 254 1.516185e-07
## 943 3.037797e-07
## 957 1.124439e-06
## 653 1.145563e-06
## 959 1.145563e-06
## 190 2.978891e-05
## 273 2.978891e-05
## 592 3.768440e-05
## 282 6.006264e-05
## 
## $go_bp
##                                       category over_represented_pvalue
## 4209            regulation of nuclear division            1.731047e-11
## 4132    regulation of mitotic nuclear division            1.123982e-09
## 1789                  mitotic nuclear division            4.001823e-09
## 2234   negative regulation of nuclear division            4.289998e-09
## 1793      mitotic sister chromatid segregation            2.999616e-08
## 409            cell cycle checkpoint signaling            3.389289e-08
## 2592                         organelle fission            3.721101e-08
## 3811      regulation of chromosome segregation            4.867973e-08
## 2005 negative regulation of cell cycle process            5.610048e-08
## 4885              sister chromatid segregation            5.876191e-08
##      under_represented_pvalue numDEInCat numInCat          FDR
## 4209                        1         38      122 9.203976e-08
## 4132                        1         32      104 2.988106e-06
## 1789                        1         57      260 5.702480e-06
## 2234                        1         22       58 5.702480e-06
## 1793                        1         44      185 2.826442e-05
## 409                         1         44      187 2.826442e-05
## 2592                        1         78      426 2.826442e-05
## 3811                        1         33      124 2.851121e-05
## 2005                        1         57      280 2.851121e-05
## 4885                        1         49      224 2.851121e-05
## 
## [1] "PrS_day_6_nor_PPARG_PTC_down"
## $reactome
##                                                                      category
## 1127                                     slc mediated transmembrane transport
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 456                                                       gpcr ligand binding
## 172                                        class a 1 rhodopsin like receptors
## 629                                                metal ion slc transporters
## 150                            cell surface interactions at the vascular wall
## 699                                                  neutrophil degranulation
## 402                                               g alpha z signalling events
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1127            1.156371e-06                0.9999995         52      185
## 1276            1.365680e-06                0.9999997         24       60
## 456             1.872841e-05                0.9999911         58      230
## 172             3.268085e-05                0.9999861         41      148
## 629             1.254404e-04                0.9999798         11       23
## 150             1.402473e-04                0.9999468         28       96
## 699             1.866653e-04                0.9998893         81      388
## 402             2.065241e-04                0.9999461         16       43
##               FDR
## 1127 0.0009047627
## 1276 0.0009047627
## 456  0.0082717150
## 172  0.0108255303
## 629  0.0309712885
## 150  0.0309712885
## 699  0.0342055552
## 402  0.0342055552
## 
## $go_bp
##                                                                       category
## 4891                                         skeletal muscle organ development
## 3063                            positive regulation of lipid catabolic process
## 4056                                          regulation of lipid localization
## 51   adenylate cyclase modulating g protein coupled receptor signaling pathway
## 1874                                                  muscle organ development
## 4926                                        sodium ion transmembrane transport
## 4927                                                      sodium ion transport
## 456                                          cellular ketone metabolic process
## 2601                                                   organic anion transport
## 3066                            positive regulation of lipid metabolic process
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4891            4.017334e-08                1.0000000         46      142
## 3063            4.450768e-08                1.0000000         12       16
## 4056            1.613051e-07                0.9999999         42      130
## 51              8.624053e-07                0.9999997         45      150
## 1874            8.754173e-07                0.9999997         72      287
## 4926            9.139410e-07                0.9999997         38      118
## 4927            9.142938e-07                0.9999996         49      170
## 456             1.108183e-06                0.9999996         49      174
## 2601            1.406945e-06                0.9999995         78      324
## 3066            1.726383e-06                0.9999994         35      109
##               FDR
## 4891 0.0001183237
## 3063 0.0001183237
## 4056 0.0002858865
## 51   0.0006944714
## 1874 0.0006944714
## 4926 0.0006944714
## 4927 0.0006944714
## 456  0.0007365260
## 2601 0.0008311917
## 3066 0.0009179178
## 
## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor_up"
## $reactome
##                                                                                           category
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 155                                                                            cellular senescence
## 189                                                           condensation of prophase chromosomes
## 955                                                                           rho gtpase effectors
## 707                                                         non integrin membrane ecm interactions
## 464                                                                     hdacs deacetylate histones
## 962                                                                      rho gtpases activate pkns
## 1040                                                senescence associated secretory phenotype sasp
## 755                                                            oxidative stress induced senescence
## 163                          chromatin modifications during the maternal to zygotic transition mzt
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13              8.238030e-11                        1         28       58
## 155             9.220637e-11                        1         58      182
## 189             1.291433e-10                        1         30       66
## 955             1.321028e-10                        1         80      293
## 707             2.201600e-10                        1         27       53
## 464             6.268639e-10                        1         35       89
## 962             6.977718e-10                        1         34       85
## 1040            8.580686e-10                        1         38      102
## 755             1.094995e-09                        1         41      114
## 163             1.227383e-09                        1         28       63
##               FDR
## 13   4.369298e-08
## 155  4.369298e-08
## 189  4.369298e-08
## 955  4.369298e-08
## 707  5.825434e-08
## 464  1.318789e-07
## 962  1.318789e-07
## 1040 1.419031e-07
## 755  1.609642e-07
## 163  1.623827e-07
## 
## $go_bp
##                                                 category
## 1239                                 heart morphogenesis
## 4161          regulation of myeloid cell differentiation
## 82                         ameboidal type cell migration
## 4673                     response to mechanical stimulus
## 3137 positive regulation of myeloid cell differentiation
## 4552                            renal system development
## 3484 protein localization to cenp a containing chromatin
## 948                        epithelial cell proliferation
## 185                            astrocyte differentiation
## 2610                                        ossification
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1239            1.619249e-08                1.0000000         58      196
## 4161            3.779471e-08                1.0000000         47      152
## 82              1.259070e-07                1.0000000         85      355
## 4673            9.082445e-07                0.9999997         44      151
## 3137            9.984315e-07                0.9999997         26       70
## 4552            1.230168e-06                0.9999996         62      242
## 3484            2.224181e-06                0.9999998         11       18
## 948             2.756074e-06                0.9999988         74      316
## 185             3.086348e-06                0.9999992         23       60
## 2610            3.116378e-06                0.9999986         76      325
##               FDR
## 1239 8.609545e-05
## 4161 1.004772e-04
## 82   2.231492e-04
## 4673 1.061732e-03
## 3137 1.061732e-03
## 4552 1.090134e-03
## 3484 1.467624e-03
## 948  1.467624e-03
## 185  1.467624e-03
## 2610 1.467624e-03
## 
## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor_down"
## $reactome
##                                  category over_represented_pvalue
## 1125 slc mediated transmembrane transport            1.818775e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 1125                0.9999927         37      163 0.02406239
## 
## $go_bp
##                                  category over_represented_pvalue
## 2599 organic acid transmembrane transport            2.081206e-06
## 2601              organic anion transport            3.930837e-06
## 2472         neutral amino acid transport            6.989340e-06
## 2600               organic acid transport            2.319466e-05
## 850              electron transport chain            2.809373e-05
## 1333        import across plasma membrane            3.739141e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 2599                0.9999993         30      113 0.01045013
## 2601                0.9999983         56      282 0.01045013
## 2472                0.9999986         16       44 0.01238744
## 2600                0.9999898         45      223 0.02987487
## 850                 0.9999889         34      152 0.02987487
## 1333                0.9999860         30      130 0.03313502
## 
## [1] "PrS_day_6_EPAS1_KO_hyp_vs_nor_up"
## $reactome
##                                                         category
## 343                            extracellular matrix organization
## 184                                           collagen formation
## 182                                 collagen chain trimerization
## 181                  collagen biosynthesis and modifying enzymes
## 515                           integrin cell surface interactions
## 183                                         collagen degradation
## 56                                       amyloid fiber formation
## 84  assembly of collagen fibrils and other multimeric structures
## 250                      degradation of the extracellular matrix
## 304                                            ecm proteoglycans
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 343            2.084585e-09                1.0000000         45      210
## 184            5.551136e-09                1.0000000         23       69
## 182            1.968568e-08                1.0000000         15       33
## 181            3.384177e-08                1.0000000         19       54
## 515            7.811981e-08                1.0000000         19       58
## 183            3.050528e-07                1.0000000         16       44
## 56             3.338554e-07                0.9999999         22       90
## 84             4.173698e-07                0.9999999         16       44
## 250            4.639578e-07                0.9999999         25       97
## 304            1.638737e-06                0.9999997         17       56
##              FDR
## 343 2.757905e-06
## 184 3.672077e-06
## 182 8.681387e-06
## 181 1.119317e-05
## 515 2.067050e-05
## 183 6.309868e-05
## 56  6.309868e-05
## 84  6.820179e-05
## 250 6.820179e-05
## 304 2.168049e-04
## 
## $go_bp
##                                           category over_represented_pvalue
## 1239                           heart morphogenesis            1.453211e-12
## 4693                     response to oxygen levels            1.869788e-09
## 1877                     muscle tissue development            9.244863e-09
## 2642                 pattern specification process            2.628106e-08
## 1022 external encapsulating structure organization            3.822076e-08
## 645                   collagen fibril organization            1.506763e-07
## 5000            striated muscle tissue development            2.173456e-07
## 948                  epithelial cell proliferation            2.766740e-07
## 1875                    muscle organ morphogenesis            3.016591e-07
## 353            cardiac muscle tissue morphogenesis            3.242813e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1239                1.0000000         49      193 7.726723e-09
## 4693                1.0000000         53      270 4.970831e-06
## 1877                1.0000000         57      312 1.638498e-05
## 2642                1.0000000         52      279 3.493409e-05
## 1022                1.0000000         43      216 4.064396e-05
## 645                 1.0000000         17       48 1.335243e-04
## 5000                0.9999999         38      185 1.650895e-04
## 948                 1.0000000         53      312 1.724203e-04
## 1875                0.9999999         18       54 1.724203e-04
## 353                 1.0000000         15       39 1.724203e-04
## 
## [1] "PrS_day_6_EPAS1_KO_hyp_vs_nor_down"
## $reactome
##                                                                                                              category
## 1202                                                     the citric acid tca cycle and respiratory electron transport
## 943  respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 94                                                                          auf1 hnrnp d0 binds and destabilizes mrna
## 621                                                                                          metabolism of polyamines
## 2                                                                              abc family proteins mediated transport
## 942                                                                                    respiratory electron transport
## 3                                                                                           abc transporter disorders
## 234                                                                    dectin 1 mediated noncanonical nf kb signaling
## 248                                                                                                degradation of dvl
## 209                                                        cross presentation of soluble exogenous antigens endosomes
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1202            7.661333e-08                1.0000000         43      171
## 943             8.596400e-08                1.0000000         35      125
## 94              9.254662e-07                0.9999998         19       52
## 621             1.774633e-06                0.9999996         19       54
## 2               2.270539e-06                0.9999994         25       86
## 942             3.143185e-06                0.9999990         28      103
## 3               4.104800e-06                0.9999990         21       67
## 234             4.565718e-06                0.9999990         19       57
## 248             6.092786e-06                0.9999987         18       53
## 209             6.974557e-06                0.9999987         16       44
##               FDR
## 1202 5.686519e-05
## 943  5.686519e-05
## 94   4.081306e-04
## 621  5.869600e-04
## 2    6.007847e-04
## 942  6.930723e-04
## 3    7.550557e-04
## 234  7.550557e-04
## 248  8.956395e-04
## 209  9.227339e-04
## 
## $go_bp
##                                                 category
## 2552           nucleoside triphosphate metabolic process
## 922  energy derivation by oxidation of organic compounds
## 2550        nucleoside triphosphate biosynthetic process
## 2629                           oxidative phosphorylation
## 466                                 cellular respiration
## 850                             electron transport chain
## 64                                   aerobic respiration
## 188                                atp metabolic process
## 3555                      proton transmembrane transport
## 189             atp synthesis coupled electron transport
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2552            2.295620e-11                        1         46      163
## 922             3.532973e-10                        1         63      285
## 2550            1.928429e-09                        1         35      118
## 2629            5.003667e-09                        1         37      133
## 466             6.508211e-09                        1         50      217
## 850             1.118979e-08                        1         39      149
## 64              2.310596e-08                        1         43      177
## 188             2.365917e-08                        1         34      123
## 3555            3.302985e-08                        1         33      119
## 189             3.587529e-08                        1         28       91
##               FDR
## 2552 1.220581e-07
## 922  9.392408e-07
## 2550 3.417820e-06
## 2629 6.651124e-06
## 466  6.920831e-06
## 850  9.916015e-06
## 64   1.572447e-05
## 188  1.572447e-05
## 3555 1.907489e-05
## 189  1.907489e-05
## 
## [1] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_up"
## $reactome
##                                                   category
## 515                     integrin cell surface interactions
## 343                      extracellular matrix organization
## 304                                      ecm proteoglycans
## 707                 non integrin membrane ecm interactions
## 250                degradation of the extracellular matrix
## 184                                     collagen formation
## 182                           collagen chain trimerization
## 28  activation of the ap 1 family of transcription factors
## 181            collagen biosynthesis and modifying enzymes
## 606                           met activates ptk2 signaling
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 515            4.862183e-07                0.9999999         21       61
## 343            5.502307e-07                0.9999998         49      221
## 304            1.609856e-06                0.9999997         20       59
## 707            2.103549e-06                0.9999996         19       55
## 250            1.345089e-05                0.9999956         27      102
## 184            2.853219e-05                0.9999919         21       73
## 182            5.203381e-05                0.9999901         13       35
## 28             8.066516e-05                0.9999961          6        9
## 181            8.138881e-05                0.9999786         17       57
## 606            9.192772e-05                0.9999846         11       28
##              FDR
## 515 0.0003639776
## 343 0.0003639776
## 304 0.0006957487
## 707 0.0006957487
## 250 0.0035591067
## 184 0.0062913484
## 182 0.0098343893
## 28  0.0119641550
## 181 0.0119641550
## 606 0.0121620375
## 
## $go_bp
##                                category over_represented_pvalue
## 5000 striated muscle tissue development            6.584172e-10
## 1239                heart morphogenesis            9.987710e-10
## 1877          muscle tissue development            1.095939e-09
## 2642      pattern specification process            7.192464e-09
## 165             appendage morphogenesis            1.343591e-08
## 164               appendage development            6.110382e-08
## 363       cardiac ventricle development            1.139033e-07
## 1874           muscle organ development            5.503470e-07
## 4896      skeletal system morphogenesis            6.600029e-07
## 659       connective tissue development            7.472347e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 5000                1.0000000         52      192 1.942369e-06
## 1239                1.0000000         53      200 1.942369e-06
## 1877                1.0000000         73      324 1.942369e-06
## 2642                1.0000000         68      304 9.560583e-06
## 165                 1.0000000         34      112 1.428775e-05
## 164                 1.0000000         38      141 5.414817e-05
## 363                 1.0000000         31       98 8.651773e-05
## 1874                1.0000000         56      265 3.604480e-04
## 4896                0.9999998         40      164 3.604480e-04
## 659                 0.9999998         49      220 3.604480e-04
## 
## [1] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_down"
## $reactome
##                                                                                                              category
## 943  respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 1202                                                     the citric acid tca cycle and respiratory electron transport
## 942                                                                                    respiratory electron transport
## 187                                                                                              complex i biogenesis
## 371                                                                         formation of atp by chemiosmotic coupling
## 94                                                                          auf1 hnrnp d0 binds and destabilizes mrna
## 151                                                                              cellular response to chemical stress
## 2                                                                              abc family proteins mediated transport
## 643                                                                                         mitochondrial translation
## 207                                                                                                 cristae formation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 943             8.068830e-16                1.0000000         56      125
## 1202            8.890067e-14                1.0000000         64      171
## 942             6.550290e-12                1.0000000         44      103
## 187             7.197179e-07                0.9999998         24       57
## 371             1.152116e-06                0.9999999         12       18
## 94              6.231576e-06                0.9999985         21       52
## 151             7.216446e-06                0.9999968         51      194
## 2               7.478901e-06                0.9999976         30       92
## 643             9.913609e-06                0.9999967         31       94
## 207             1.018834e-05                0.9999983         15       31
##               FDR
## 943  1.067506e-12
## 1202 5.880779e-11
## 942  2.888678e-09
## 187  2.380467e-04
## 371  3.048500e-04
## 94   1.236823e-03
## 151  1.236823e-03
## 2    1.236823e-03
## 643  1.347917e-03
## 207  1.347917e-03
## 
## $go_bp
##                                                 category
## 2629                           oxidative phosphorylation
## 850                             electron transport chain
## 64                                   aerobic respiration
## 466                                 cellular respiration
## 189             atp synthesis coupled electron transport
## 4571                respiratory electron transport chain
## 922  energy derivation by oxidation of organic compounds
## 2552           nucleoside triphosphate metabolic process
## 3554            proton motive force driven atp synthesis
## 2550        nucleoside triphosphate biosynthetic process
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2629            4.584301e-18                        1         59      133
## 850             3.869701e-16                        1         61      153
## 64              1.685665e-15                        1         66      178
## 466             1.968407e-15                        1         75      219
## 189             1.992795e-15                        1         44       91
## 4571            2.686586e-14                        1         48      112
## 922             1.967939e-13                        1         85      289
## 2552            4.729783e-12                        1         57      167
## 3554            4.837058e-12                        1         35       74
## 2550            2.013260e-11                        1         45      118
##               FDR
## 2629 2.437473e-14
## 850  1.028760e-12
## 64   2.119138e-12
## 466  2.119138e-12
## 189  2.119138e-12
## 4571 2.380763e-11
## 922  1.494791e-10
## 2552 2.857626e-09
## 3554 2.857626e-09
## 2550 1.070450e-08
## 
## [1] "PrS_day_6_WT_WT_hyp_vs_nor_up"
## $reactome
##                                                                                           category
## 466                                                                     hdacs deacetylate histones
## 56                                                                         amyloid fiber formation
## 606                                                                          meiotic recombination
## 282                                                                                dna methylation
## 86                                        assembly of the orc complex at the origin of replication
## 13   activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 254                               deposition of new cenpa containing nucleosomes at the centromere
## 1125                                                    sirt1 negatively regulates rrna expression
## 190                                                           condensation of prophase chromosomes
## 757                                                            oxidative stress induced senescence
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 466             1.839398e-12                        1         40       90
## 56              9.165630e-12                        1         40       94
## 606             8.444486e-11                        1         35       79
## 282             1.262692e-10                        1         29       59
## 86              1.407572e-10                        1         30       63
## 13              1.584806e-10                        1         29       60
## 254             2.570763e-10                        1         31       68
## 1125            4.278800e-10                        1         29       62
## 190             7.900714e-10                        1         30       67
## 757             1.034177e-09                        1         44      117
##               FDR
## 466  2.437203e-09
## 56   6.072230e-09
## 606  3.499781e-08
## 282  3.499781e-08
## 86   3.499781e-08
## 13   3.499781e-08
## 254  4.866086e-08
## 1125 7.086763e-08
## 190  1.163161e-07
## 757  1.370285e-07
## 
## $go_bp
##                                                             category
## 2642                                   pattern specification process
## 1293 homophilic cell adhesion via plasma membrane adhesion molecules
## 398        cell cell adhesion via plasma membrane adhesion molecules
## 1239                                             heart morphogenesis
## 164                                            appendage development
## 165                                          appendage morphogenesis
## 5000                              striated muscle tissue development
## 214                                                    axon guidance
## 1022                   external encapsulating structure organization
## 1877                                       muscle tissue development
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2642            1.964648e-12                1.0000000        109      338
## 1293            3.272453e-12                1.0000000         62      137
## 398             2.139354e-11                1.0000000         81      215
## 1239            4.214341e-09                1.0000000         72      217
## 164             1.404575e-08                1.0000000         52      146
## 165             2.424452e-08                1.0000000         44      116
## 5000            3.850266e-08                1.0000000         67      209
## 214             1.272362e-07                0.9999999         60      182
## 1022            2.726303e-07                1.0000000         76      260
## 1877            2.893302e-07                1.0000000         95      348
##               FDR
## 2642 8.699815e-09
## 1293 8.699815e-09
## 398  3.791649e-08
## 1239 5.601913e-06
## 164  1.493625e-05
## 165  2.148468e-05
## 5000 2.924552e-05
## 214  8.456437e-05
## 1022 1.538369e-04
## 1877 1.538369e-04
## 
## [1] "PrS_day_6_WT_WT_hyp_vs_nor_down"
## $reactome
##                                                                                                              category
## 152                                                                              cellular response to chemical stress
## 730                                                                                 nuclear events mediated by nfe2l2
## 568                                                                                              keap1 nfe2l2 pathway
## 623                                                                                          metabolism of polyamines
## 94                                                                          auf1 hnrnp d0 binds and destabilizes mrna
## 945  respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 210                                                        cross presentation of soluble exogenous antigens endosomes
## 1204                                                     the citric acid tca cycle and respiratory electron transport
## 250                                                                                                degradation of dvl
## 944                                                                                    respiratory electron transport
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 152             4.182472e-09                1.0000000         83      197
## 730             5.610407e-09                1.0000000         48       94
## 568             9.025730e-09                1.0000000         57      121
## 623             1.767221e-08                1.0000000         33       56
## 94              3.459032e-08                1.0000000         31       52
## 945             3.976105e-08                1.0000000         58      126
## 210             1.080434e-07                1.0000000         27       44
## 1204            1.279762e-07                0.9999999         72      173
## 250             2.935247e-07                0.9999999         30       53
## 944             3.594945e-07                0.9999999         48      103
##               FDR
## 152  3.716895e-06
## 730  3.716895e-06
## 568  3.986364e-06
## 623  5.853920e-06
## 94   8.780565e-06
## 945  8.780565e-06
## 210  2.045106e-05
## 1204 2.119607e-05
## 250  4.321336e-05
## 944  4.763301e-05
## 
## $go_bp
##                                                 category
## 3555                      proton transmembrane transport
## 922  energy derivation by oxidation of organic compounds
## 4783                                 ribosome biogenesis
## 2629                           oxidative phosphorylation
## 4612            response to endoplasmic reticulum stress
## 850                             electron transport chain
## 189             atp synthesis coupled electron transport
## 466                                 cellular respiration
## 4571                respiratory electron transport chain
## 64                                   aerobic respiration
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3555            1.781999e-10                        1         61      129
## 922             4.902791e-10                        1        111      298
## 4783            1.191437e-09                        1        115      315
## 2629            9.222683e-09                        1         60      136
## 4612            1.047022e-08                        1         91      244
## 850             1.518248e-08                        1         66      157
## 189             2.325707e-08                        1         45       93
## 466             4.964408e-08                        1         84      224
## 4571            6.267356e-08                        1         51      114
## 64              9.493106e-08                        1         72      183
##               FDR
## 3555 9.474888e-07
## 922  1.303407e-06
## 4783 2.111624e-06
## 2629 1.113403e-05
## 4612 1.113403e-05
## 850  1.345421e-05
## 189  1.766541e-05
## 466  3.299470e-05
## 4571 3.702615e-05
## 64   5.047484e-05
enrichment_output_dir = file.path(result_dir, "enrichment")

if (!file.exists(enrichment_output_dir)){
  dir.create(enrichment_output_dir, recursive = TRUE)
}

saveRDS(goseq_res, 
        file.path(enrichment_output_dir, 
                  sprintf("%s_enrichment.rds", release_name)))  
gc()
##            used  (Mb) gc trigger  (Mb) max used  (Mb)
## Ncells  8884314 474.5   16044431 856.9 16044431 856.9
## Vcells 20446264 156.0   73524670 561.0 73524670 561.0
sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.6 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /app/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib/libflexiblas.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0
##  [2] GenomicFeatures_1.46.1                  
##  [3] GenomicRanges_1.46.1                    
##  [4] GenomeInfoDb_1.30.1                     
##  [5] org.Hs.eg.db_3.14.0                     
##  [6] AnnotationDbi_1.56.2                    
##  [7] IRanges_2.28.0                          
##  [8] S4Vectors_0.32.4                        
##  [9] Biobase_2.54.0                          
## [10] BiocGenerics_0.40.0                     
## [11] data.table_1.14.2                       
## [12] dplyr_1.0.7                             
## [13] fgsea_1.20.0                            
## [14] goseq_1.46.0                            
## [15] geneLenDataBase_1.30.0                  
## [16] BiasedUrn_1.07                          
## [17] RColorBrewer_1.1-2                      
## [18] stringr_1.4.0                           
## [19] ggpubr_0.4.0                            
## [20] ggrepel_0.9.1                           
## [21] ggplot2_3.5.1                           
## [22] rmarkdown_2.11                          
## 
## loaded via a namespace (and not attached):
##   [1] colorspace_2.0-2            ggsignif_0.6.3             
##   [3] rjson_0.2.20                ellipsis_0.3.2             
##   [5] rio_0.5.27                  XVector_0.34.0             
##   [7] bit64_4.0.5                 fansi_0.5.0                
##   [9] xml2_1.3.2                  splines_4.1.2              
##  [11] cachem_1.0.6                knitr_1.36                 
##  [13] jsonlite_1.7.2              Cairo_1.5-12.2             
##  [15] Rsamtools_2.10.0            broom_0.7.10               
##  [17] GO.db_3.14.0                dbplyr_2.1.1               
##  [19] png_0.1-7                   compiler_4.1.2             
##  [21] httr_1.4.2                  backports_1.3.0            
##  [23] assertthat_0.2.1            Matrix_1.6-4               
##  [25] fastmap_1.1.0               cli_3.6.3                  
##  [27] htmltools_0.5.2             prettyunits_1.1.1          
##  [29] tools_4.1.2                 gtable_0.3.0               
##  [31] glue_1.4.2                  GenomeInfoDbData_1.2.7     
##  [33] rappdirs_0.3.3              fastmatch_1.1-3            
##  [35] Rcpp_1.0.7                  carData_3.0-4              
##  [37] cellranger_1.1.0            jquerylib_0.1.4            
##  [39] vctrs_0.6.5                 Biostrings_2.62.0          
##  [41] nlme_3.1-153                rtracklayer_1.54.0         
##  [43] xfun_0.27                   openxlsx_4.2.4             
##  [45] lifecycle_1.0.4             restfulr_0.0.13            
##  [47] rstatix_0.7.0               XML_3.99-0.8               
##  [49] zlibbioc_1.40.0             scales_1.3.0               
##  [51] hms_1.1.1                   MatrixGenerics_1.6.0       
##  [53] parallel_4.1.2              SummarizedExperiment_1.24.0
##  [55] yaml_2.2.1                  curl_4.3.2                 
##  [57] gridExtra_2.3               memoise_2.0.0              
##  [59] sass_0.4.0                  biomaRt_2.50.3             
##  [61] stringi_1.7.5               RSQLite_2.2.8              
##  [63] highr_0.9                   BiocIO_1.4.0               
##  [65] filelock_1.0.3              zip_2.2.0                  
##  [67] BiocParallel_1.28.3         rlang_1.1.4                
##  [69] pkgconfig_2.0.3             matrixStats_1.3.0          
##  [71] bitops_1.0-7                evaluate_0.14              
##  [73] lattice_0.20-45             purrr_0.3.4                
##  [75] GenomicAlignments_1.30.0    bit_4.0.4                  
##  [77] tidyselect_1.1.1            magrittr_2.0.1             
##  [79] R6_2.5.1                    generics_0.1.3             
##  [81] DelayedArray_0.20.0         DBI_1.1.1                  
##  [83] mgcv_1.8-38                 pillar_1.6.4               
##  [85] haven_2.4.3                 foreign_0.8-81             
##  [87] withr_3.0.0                 KEGGREST_1.34.0            
##  [89] abind_1.4-5                 RCurl_1.98-1.5             
##  [91] tibble_3.1.5                crayon_1.4.2               
##  [93] car_3.0-11                  utf8_1.2.2                 
##  [95] BiocFileCache_2.2.1         progress_1.2.2             
##  [97] grid_4.1.2                  readxl_1.3.1               
##  [99] blob_1.2.2                  forcats_0.5.1              
## [101] digest_0.6.28               tidyr_1.1.4                
## [103] munsell_0.5.0               bslib_0.3.1